Compositions and methods for treatment of disorders related to CEP290

ABSTRACT

Compositions are provided that comprise a recombinant vector carrying a nucleic acid sequence encoding a fragment of CEP290 lacking all or part of its N-terminal and C-terminal inhibitory regions, under the control of regulatory sequences which express the product of said gene in a selected cell of a mammalian subject, and a pharmaceutically acceptable carrier. These and other compositions are disclosed with are useful in methods for treating a mammalian subject having a disease associated with a CEP290 mutation, such as Lebers Congenital Amaurosis.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a divisional of U.S. patent application Ser. No.14/904,447, filed Jan. 12, 2016, which is a national stage ofInternational Patent application No. PCT/US14/046408, filed Jul. 11,2014 (expired), which claims the benefit of the priority of U.S.Provisional Patent Application No. 61/847,016, filed Jul. 16, 2013. Thepriority applications are incorporated herein by reference.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with government support under Grant Nos.R24EY019861 and 8DP1EY023177 awarded by the National Institutes ofHealth. The government has certain rights in this invention.

INCORPORATION-BY-REFERENCE OF MATERIAL SUBMITTED IN ELECTRONIC FORM

Applicant hereby incorporates by reference the Sequence Listing materialfiled in electronic form herewith. This file is labeled“UPN-Y6321USD1_ST25.txt”.

BACKGROUND OF THE INVENTION

Defects in primary cilium formation and function are responsible for avariety of human diseases and developmental disorders, collectivelytermed ciliopathies. While the ciliopathies are diverse in bothphenotype and etiology, specific genes, including CEP290, have beenimplicated as having causative roles in multiple cilium-associateddisorders. Mutations in the gene CEP290 have been described in up to 20%of cases of the devastating inherited blinding disease Leber congenitalamaurosis and in numerous cases of other more debilitating ciliopathies,such as Joubert syndrome, Senior Loken Syndrome, and Meckel-Grubersyndrome. These disorders range in severity from isolated retinaldegeneration to renal dysfunction, central nervous system malformations,hepatic development defects, and embryonic lethality.

Attempts to treat genetic defects have been attempted by delivery ofnormal genes to the cells expressing the defective genes, such asrecombinant adeno-associated virus (AAV)-based therapeutics. See, e.g.,U.S. Pat. No. 8,147,823. Generally, large gene sequences have beendifficult to fit effectively into some of the more useful vectordelivery systems. The extension, to CEP290 patients, of recombinantadeno-associated virus (AAV)-based therapeutics, which have proven safeand effective in the treatment of another genetic cause of LCA, has beenhindered by CEP290's large size, precluding it from packaging in AAV.

There remains a need in the art for additional therapeutic compositionsand methods for treatment of LCA and other ciliopathies.

SUMMARY OF THE INVENTION

In one aspect, a composition comprises a recombinant vector carrying anucleic acid sequence encoding a fragment of the CEP290 gene lacking allor portions of at least one of its N-terminal and C-terminal inhibitoryregions. The CEP290 fragment is under the control of regulatorysequences which express the product of the gene in a selected cell of amammalian subject, and a pharmaceutically acceptable carrier.Embodiments comprise nucleic acid sequences of CEP290 which includecontinuous fragments of CEP290 or discontinuous fragments of CEP290spliced together in the same reading frame. In one embodiment, thenucleic acid sequence comprises a sequence encoding amino acids 1695 to1966 (SEQ ID NO: 53) of CEP290, i.e., aa1695 to 1966 of SEQ ID NO: 2. Instill another embodiment, the vector of the compositions is anadeno-associated vector.

In another aspect, a composition comprises a recombinantadeno-associated vector carrying a nucleic acid sequence encoding afragment of the CEP290 gene lacking at least one of its N-terminal andC-terminal inhibitory regions, under the control of regulatory sequenceswhich express the product of said gene in a photoreceptor cell of amammalian subject, and a pharmaceutically acceptable carrier.

In another aspect, a synthetic or recombinant protein is disclosed thatcomprises discontinuous CEP290 amino acid fragments spliced together ina single open reading frame. This synthetic protein has biologicalactivity that mimics the biological activity of normal full lengthCEP290. In certain embodiments, the discontinuous CEP290 amino acidfragments are one or more of aa130 to 380 (SEQ ID NO: 49), aa700 to 1040(SEQ ID NO: 51), aa1260 to 1605 (SEQ ID NO: 52), aa1695 to 1990 (SEQ IDNO: 54), aa 1695 to 1966 (SEQ ID NO: 53) of CEP290, or aa 1695 to 1995(SEQ ID NO: 55) of CEP290 of SEQ ID NO: 2 or 4. In another embodiment,the synthetic or recombinant protein has the sequence of SEQ ID NO: 6.

In another aspect, a synthetic or recombinant nucleic acid sequence isprovided that encodes the above-referenced protein comprisingdiscontinuous CEP290 amino acid fragments spliced together in a singleopen reading frame.

In another aspect, compositions containing the synthetic or recombinantprotein or nucleic acid sequences also contain therapeuticallyacceptable carriers. Such compositions may include the vectors abovewhich carry the nucleic acid sequences, or other components.

In yet another aspect, a method of treating a mammalian subject having adisease associated with a CEP290 mutation or defect in the CEP290 gene,protein or expression levels is provided. The method comprisesadministering to said subject an effective concentration of any of thecompositions as described above and in further detail in thespecification. This method can involve administering a composition asdescribed herein to cells of the retina, e.g., photoreceptors, thecentral nervous system, the brain, kidney, bone or olfactory epithelium.

In still another aspect, a method of preventing, arresting progressionof or ameliorating vision loss associated with Lebers CongenitalAmaurosis in a subject is provided. The method comprises administeringto a mammalian subject in need thereof an effective concentration of anyof the compositions described herein. In one embodiment, the compositioncomprises a recombinant adeno-associated virus (AAV) carrying a nucleicacid sequence encoding a fragment of the CEP290 gene lacking at leastone of its N-terminal and C-terminal inhibitory regions, under thecontrol of regulatory sequences which express the product of said genein a photoreceptor cell of a mammalian subject, and a pharmaceuticallyacceptable carrier.

Other aspects of the invention and disclosure are described in thefollowing detailed description.

BRIEF DESCRIPTION OF THE FIGURES

FIGS. 1A to 1E illustrate that CEP290 aa 1 to 380 (SEQ ID NO: 46), i.e.,aa 1 to 380 of SEQ ID NO: 2, mediate membrane association. FIG. 1A is ascale representation of human CEP290 SEQ ID NO: 2. Known human CEP290mutations are noted by tick marks. The indicated domains and mutationsare adapted from reference 30. FIG. 1B are fluorescence microscopyimages showing the localization pattern of GFP fusions of full length(FL) and truncated CEP290 constructs in hTERT-RPE1 cells. Cells werestained for ARL13B and with DAPI. Scale bars are 5 μm. Insets show 3×magnified views of areas (in boxes) of colocalization between CEP290truncations and ARL13B. FIG. 1C show representative membrane flotationassay performed on hTERT-RPE1 cells overexpressing CEP290 aa 1 to 580(SEQ ID NO: 47) of SEQ ID NO: 2. Equal amounts of each of fivefractions, beginning from the top (1) and ending at the bottom (8) ofthe sucrose gradient were analyzed. The sucrose percentage and theexpected protein composition of each fraction are indicated. Blots wereprobed for GFP to detect CEP290 aa 1 to 580 and for the indicatedcontrols. Relevant molecular weight markers are shown in kDa. FIG. 1Dshows that ARL13B positive vesicles were immunoprecipitated frompostnuclear supernatants of hTERT-RPE1 cells expressing the indicatedCEP290 truncations or GFP alone. The input, unbound fraction (UB) andimmunoprecipitated fraction (IP) were probed with an anti-GFP antibodyto detect our truncations. Relevant molecular weight markers are shownin kDa. FIG. 1E show the peripheral membrane (Peri.) and integralmembrane protein (Int.) fractions of hTERTRPE1 cells expressing theindicated CEP290 truncations that were isolated and probed for GFP todetect CEP290 truncations and for the indicated controls. Relevantmolecular weight markers are shown in kDa.

FIGS. 2A to 2E illustrate that CEP290 directly binds membranes in vitroand contains a highly conserved membrane binding amphipathic α-helix.FIG. 2A are fluorescence microscopy images showing the localizationpattern of GFP fusions of full length (FL) and truncated CEP290constructs in hTERTRPE1 cells stained for LAMP2 and with DAPI. Scalebars are 5 μm. Insets show 3× magnified views of areas (in boxes)illustrating lack of colocalization between CEP290 truncations andLAMP2. FIG. 2B shows the results of subcellular fractionationexperiments performed on 293T cells expressing CEP290 constructs. Cellswere fractionated into cytoplasmic (C), membrane (M), nuclear (N), andcytoskeletal (S) fractions and analyzed by western blotting. Relevantmolecular weight markers are shown in kDa. FIG. 2C shows the percent ofeach truncation present in the membrane fraction. Data are presented asmean±SD, n=3. Asterisks indicate statistical significance over GFPalone. FIG. 2D show the results of liposome co-flotation assaysperformed on purified CEP290 aa 1 to 580. Data is shown for assaysperformed with CEP290 aa 1 to 580, both with and without liposomes, andwith BSA as a control. Equal amounts of each of five fractions,beginning from the top (1) and ending at the bottom (5) of the sucrosegradient were analyzed. The sucrose percentage and the expected proteincomposition of each fraction are indicated. Relevant molecular weightmarkers are shown in kDa. FIG. 2E illustrate helical wheel projection ofCEP290 aa 257 to 292 (SEQ ID NO: 50). Darkest circles representnegatively charged amino acids; slightly less dark circles representpositively charged amino acids; the lightest grey circles representpolar, uncharged amino acids, and medium grey circles represent nonpolaramino acids. By aligning CEP290's predicted amphipathic helix fromGallus SEQ ID NO: 35, Meleagris SEQ ID NO: 36, Rattus SEQ ID NO: 37, MusSEQ ID NO: 38, Pongo SEQ ID NO: 39, Macaca SEQ ID NO: 40, Homo sapiensSEQ ID NO: 41, Felis SEQ ID NO: 42, Ailuropoda SEQ ID NO: 43 and DanioSEQ ID NO: 45, one can see there is usually conservation of polarity andcharge between the divergent residues.

FIGS. 3A to 3C show that CEP290 colocalizes with microtubules via regionM, and truncation of its N- and C-termini enhances this colocalization.FIG. 3A are fluorescence confocal microscopy images showing thelocalization pattern of GFP fusions of full length (FL) and truncatedCEP290 constructs expressed in hTERT-RPE1 cells or in HEK293T cells.Samples were stained for α-tubulin or acetylated α-tubulin, pericentrinor with DAPI. Scale bars are 10 μm. Insets show 10× magnified views ofareas of colocalization (in boxes) between CEP290 truncations andpericentrin. In all cases, truncations partially colocalize withpericentrin. In some cases, truncations colocalize with tubulin. RegionM is necessary and sufficient for tubulin colocalization. FIG. 3B arescale representations of the library of CEP290 truncations tested inFIG. 3A. Included is a summary of the extent of colocalization withtubulin, rated on a scale ranging from negative (−) to highly positive.Truncations were also in vitro transcribed and translated and subjectedto a microtubule MT sedimentation assay. The recombinantly expressed andpurified microtubule binding region of CEP290 was similarly subjected toa MT sedimentation assay. FIG. 3C illustrates that for each truncation,the percent of transfected hTERT-RPE1 cells in which the GFP fusedtruncation displayed a fibrillar localization pattern was determined. Atleast 100 transfected cells were counted per experiment. Data arepresented as mean±SD, n=3. Quantification of the different localizationpatterns of each truncation from three independent experiments. Region Mof CEP290 is necessary and sufficient for fibrillar localization. Theinclusion of the N- and C-termini diminishes the extent to whichtruncations assume a fibrillar pattern of localization.

FIGS. 4A to 4F show that CEP290 directly binds to and bundlesmicrotubules via region M, and its N- and C-termini inhibit microtubulebinding and bundling. FIG. 4A shows representative confocal fluorescencemicroscopy images of GFP fusions of full length (FL) and truncatedCEP290 constructs expressed in hTERT-RPE1 cells stained for acetylatedα-tubulin and with DAPI. Scale bars are 10 μm. Truncations containingCEP290 aa1695 to 1966 of SEQ ID NO: 2 perturb the acetylated tubulinstaining pattern in hTert-RPI and 293T cells, and deletion of the N- andC-termini enhance the effect. Confocal images of CEP290 truncationsoverexpressed in hTERT-RPE1 cells stained with an anti-acetylatedtubulin antibody. Truncations containing aa1695 to 1966 of SEQ ID NO: 2increase the intensity of acetylated tubulin staining and result in morebundles of acetylated MTs compared to untransfected cells. FIG. 4B showpercent of transfected 293T cells showing an increase in the intensity,and perturbation in pattern, of acetylated α-tubulin staining comparedto untransfected cells, following transfection with CEP290 truncations.Deletion of both the N- and C-termini, but not either alone,significantly increases the intensity of acetylated tubulin staining.100 transfected cells were counted per experiment. Data are presented asmean±SD, n=5. Means with different letters are significantly different.FIG. 4C are Western blots of microtubule (MT) co-sedimentation assaysfor in vitro transcribed and translated CEP290 truncation mutants. Theresulting supernatants (S) and microtubule pellets (P) were probed forthe presence of the GFP-fused truncations and are shown for assaysperformed both with (+MT) and without (−MT) microtubules. Relevantmolecular weight markers are shown in kDa. FIG. 4D shows the percent ofeach truncation co-sedimenting with microtubules. Quantification of thepercent of total truncation present in the MT pellet for threeindependent experiments is shown. Only minimal pelleting is observed inthe −MT controls. AA1695 to 1966 of SEQ ID NO: 2 are necessary forsignificant MT binding, and deletion of both the N- and C-termini, butnot of either alone, significantly increases MT binding. Data arepresented as mean±SD, n=3. Means with different letters aresignificantly different. The N- and C-termini cooperatively inhibit MTbinding. FIG. 4E are Coomassie-stained gel of microtubuleco-sedimentation assays performed with recombinantly expressed andpurified CEP290 truncation M subjected to a MT sedimentation assay withincreasing concentrations of microtubules (tubulin). Truncation Mdirectly binds MTs with an apparent K_(d) in the nanomolar range,comparable to other MT binding proteins. The supernatants (S) andmicrotubule pellets (P) are shown. Relevant molecular weight markers areshown in kDa. CEP290 aa1695 to 1966 of SEQ ID NO: 2 directly bind MTswith a K_(d) in the nanomolar range. FIG. 4F is a binding curve ofmicrotubule cosedimentation assays as in FIG. 4E. The fraction oftruncation M present in the pellet in the absence of microtubules wassubtracted from all data points. Data points are presented as means±SD,n=3. A curve was fit to the data points using the non-linear regressionfunctionality of the GraphPad Prism program.

FIGS. 5A to 5G show that the overexpression of either the N- orC-terminal regulatory regions of CEP290 ablates the normal inhibition ofCEP290. FIG. 5A shows fluorescence microscopy fields of hTERT-RPE1 cellstransduced with lentiviral empty vector (EV), or vectors encoding eitherthe N- (aa 1 to 580) or C-terminus (aa 1966 to 2479) of CEP290 (SEQ IDNO: 59). Cells were stained for acetylated α-tubulin and pericentrin todetect primary cilia and with DAPI. Arrowheads indicate primary cilia.Arrows indicate cells with multiple axonemes originating from the samefocus of pericentrin. Scale bars are 10 μm. FIG. 5B show the percent oflentivirus-treated cells forming primary cilia. Data are presented asmean±SD, n=3. 100 cells were counted per experiment. FIG. 5C showfluorescence microscopy images of single hTERT-RPE1 cells transducedwith lentiviral vectors as in FIG. 5A. Cells were stained for acetylatedα-tubulin to detect primary cilia and with DAPI. Scale bars are 5 μm.FIG. 5D shows the average primary cilium length for hTERT-RPE1 cells asin FIG. 5C. Data are presented as mean±SD, n=3. A total of at least 150cilia were measured per condition. FIG. 5E are fluorescence microscopyimages of hTERT-RPE1 cells that formed multiple cilia after transductionwith lentiviral vector encoding the N-terminus of CEP290. Cells werestained with acetylated α-tubulin, ARL13B, and with DAPI. Scale bars are5 μm. FIG. 5F are fluorescence microscopy images of hTERT-RPE1 cellsthat formed multiple cilia after transduction with lentiviral vectorencoding the N-terminus of CEP290. Cells were stained with acetylatedα-tubulin, pericentrin and with DAPI. Scale bars are 5 μm. FIG. 5G showsthe percent of lentivirus treated hTERT-RPE1 cells forming multiplecilia. At least 100 cells were counted per experiment. Data arepresented as mean±SD, n=3.

FIGS. 6A to 6F show that an in-frame deletion in Cep290 in the rd16mouse ablates Cep290's microtubule binding activity. FIG. 6A is aschematic representation of the microtubule binding region of humanCEP290 in relation to the rd16 mouse deletion (17). Truncations ofCEP290 representing the part of the microtubule binding region deletedin the rd16 mouse and the part of the microtubule binding regionmaintained in the rd16 mouse were created as shown. FIG. 6B are confocalfluorescence microscopy images showing the localization pattern of theGFP-tagged “Maintained” and “Deleted” CEP290 truncations. Cells werestained for α-tubulin, pericentrin and with DAPI. Scale bars are 10 μm.FIG. 6C are immunoblots of representative microtubule co-sedimentationassays for in vitro transcribed and translated “Maintained” and“Deleted” CEP290 truncations. The supernatant (S) and microtubule pellet(P) fractions are shown in assays performed both with (+MT) and without(−MT) the addition of microtubules. Relevant molecular weight markersare shown in kDa. FIG. 6D shows the percent of each truncationco-sedimenting with microtubules. Data are presented as mean±SD, n=2.FIG. 6E are representative western blots of microtubule co-sedimentationassays performed with full length WT and rd16 Cep290 from mouse brainhomogenate. The supernatant (S) and microtubule pellet (P) fractions areshown in assays performed on samples induced to polymerize microtubules(+MT) and samples treated to prevent microtubule polymerization (−MT).Relevant molecular weight markers are shown in kDa. FIG. 6F showspercent of WT and rd16 CEP290 co-sedimenting with microtubules. Data arepresented as mean±SD, n=3. Asterisks indicate statistical significanceover −MT samples.

FIG. 7A to 7E show rd16 mouse fibroblasts are deficient in primarycilium formation. FIG. 7A show fluorescence microscopy fields of WTprimary dermal fibroblasts that were stained for acetylated α-tubulin toidentify primary cilia, and stained with DAPI. Fibroblasts were grown inmedia with (Fed) or without (Starved) serum. Arrowheads indicate primarycilia. Scale bars are 10 μm. FIG. 7B show fluorescence microscopy fieldsof rd16 primary dermal fibroblasts stained for acetylated α-tubulin toidentify primary cilia, and stained with DAPI. Fibroblasts were grown inmedia with (Fed) or without (Starved) serum. Arrowheads indicate primarycilia. Scale bars are 10 μm. FIG. 7C show the percent of WT and rd16primary dermal fibroblasts that form primary cilia in serum fed andserum starved conditions. Quantification was based on separateexperiments on fibroblasts coming from 3 different animals per genotype.At least 100 cells were counted per experiment. Data are presented asmean±SD, n=5. FIG. 7D show high magnification fluorescent microscopyimages of representative serum-starved WT and rd16 primary dermalfibroblasts stained for acetylated α-tubulin to identify primary cilia,and stained with DAPI. Scale bars are 5 μm. FIG. 7E are average ciliumlength of serum starved WT and rd16 primary dermal fibroblasts.Quantification was based on separate experiments on fibroblasts comingfrom 3 different animals per genotype. At least 50 cilia were measuredper experiment, and a total of 400 cilia were measured for both the WTand rd16 fibroblasts. Data are presented as mean±SD, n=5.

FIG. 8 shows a speculative model for CEP290 activity at the primarycilium in four panels. CEP290 is maintained in a closed, inhibited stateby its N- and C-termini and CP110 during the cell cycle; CP110 bound toCEP290 with the N- and C-termini binding each other (panel A). Uponentry into Go CP110 is degraded at the mother centriole (panel B),destabilizing the closed conformation. This conformational change in theprotein frees and activates CEP290's membrane binding and microtubulebinding domains (panel C). In its open conformation, active CEP290 isable to recruit additional interacting partners including MTs and toinitiate IFT and ciliogenesis (panel D).

FIG. 9A is the nucleic acid sequence encoding full length naturallyoccurring human CEP290 SEQ ID NO: 1.

FIG. 9B is the amino acid sequence encoding full length naturallyoccurring human CEP290 SEQ ID NO: 2.

FIG. 10A is a synthetic nucleic acid sequence for codon optimized humanCEP290 SEQ ID NO: 3.

FIG. 10B is a synthetic amino acid sequence for codon optimized humanCEP290 SEQ ID NO: 4.

FIG. 11A is a synthetic construct which is a minigene for CEP290 SEQ IDNO: 5, which encodes the following CEP290 amino acid fragments, splicedtogether in a single open reading frame: aa130 to 380, aa700 to 1040,aa1260 to 1605, and aa1695 to 1990.

FIG. 11B is the synthetic amino acid sequence construct SEQ ID NO: 6encoded by FIG. 11A.

FIGS. 12A to 12C demonstrate the generation and testing of CEP290 shRNAconstructs. FIG. 12A shows hTERT-RPE1 cells transiently transfected withthree different CEP290 shRNA constructs, which were lysed and analyzedby western blotting for CEP290 levels. Blots were reprobed for GAPDH asa loading control. FIG. 12B shows densitometric quantification of CEP290protein levels in hTERT-RPE1 cells as in FIG. 12A. CEP290 levels werenormalized using GAPDH as a loading control and the percent of CEP290remaining, compared to untransfected hTERT-RPE1 cells, was determined.Immunofluorescence microscopy images of fields of hTERT-RPE1 cells,either untransfected or transfected with CEP290 shRNA construct 2, werestained for acetylated tubulin as a marker of the primary cilium (datanot shown). FIG. 12C shows the percent of control and sh2 transfectedhTERT-RPE1 cells that formed cilia upon serum starvation.

FIGS. 13A to 13C show the isolation and testing of clonal CEP290knockdown cell lines. FIG. 13A shows clonal retrovirus-transducedhTERT-RPE1 cell lines expressing CEP290 shRNA 2 that were lysed andanalyzed by western blotting for CEP290 levels. Blots were reprobed forGAPDH as a loading control. FIG. 13 B shows densitometric quantificationof CEP290 protein levels in these hTERT-RPE1 cells. CEP290 levels werenormalized using GAPDH as a loading control and the percent of CEP290remaining, compared to untransfected hTERT-RPE1 cells, was determined.Immunofluorescence microscopy images of fields of control and sh2.8hTERT-RPE1 cells stained for acetylated tubulin as a marker of theprimary cilium were obtained (data not shown). FIG. 13C shows thepercent of control and sh2.8 hTERT-RPE1 cells that formed cilia uponserum starvation.

FIGS. 14A and 14B show the construction and testing of a miniCEP290construct. FIG. 14A is a schematic representation of the CEP290 proteinwith identified functional domains, interacting domains, and proteinmotifs labeled. Grayed areas represent regions of the protein notincluded in the miniCEP290 construct. FIG. 14B is a schematicrepresentation of miniCEP290. Immunofluorescence images of hTERT-RPE1cells transiently transfected with GFP-fused miniCEP290 and stained foracetylated tubulin and pericentrin, and with DAPI were obtained, andshowed the localization of miniCEP290 to the ciliary transition zone(data not shown).

DETAILED DESCRIPTION OF THE INVENTION

CEP290 is a vital structural and regulatory element of the ciliarytransition zone, elucidation of its molecular functionality at thecenter of the critically important and disease-relevant pathways ofciliogenesis and IFT. The inventors have identified novel regulatorydomains of CEP290 useful in therapeutic interventions for diseases ofthe cilia caused by mutated CEP290. Truncation mutants or fragments ofCEP290 lacking certain of the novel inhibitory domains but maintainingthe other functional regions of the protein exhibit normal, or evenenhanced, CEP290 function, while at the same time being small enough tofit in certain vectors, such as AAV. The delivery of such a therapeuticto terminally differentiated tissues, such as the retina, to effectpermanent activation of CEP290 is useful in the treatment ofCEP290-related diseases, such as LCA. The delivery of such a therapeuticis also useful to treat other diseases caused by naturally mutated ornon-functional CEP290 in other tissues, such as the brain or kidney orbone.

Four novel functional domains of the CEP290 protein are identified,showing that CEP290 directly binds to the cellular membrane via anN-terminal domain that includes a highly conserved amphipathic helixmotif, and directly binds to microtubules through a domain locatedwithin its myosin-tail homology domain. Furthermore, CEP290 activity wasfound to be regulated by two novel autoinhibitory domains within its N-and C-termini, both of which were also found to play critical roles inregulating ciliogenesis. Disruption of the novel microtubule bindingdomain in the rd16 mouse LCA model was found to be sufficient to inducesignificant deficits in cilium formation leading to retinaldegeneration. Various compositions and treatment methods forCEP290-related diseases utilizing these domains are disclosed.

In one embodiment, a composition comprises a recombinant vector carryinga nucleic acid sequence encoding a fragment of the CEP290 gene lackingat least one of its N-terminal and C-terminal inhibitory regions, underthe control of regulatory sequences which express the product of saidgene in a selected cell of a mammalian subject, and a pharmaceuticallyacceptable carrier. In another embodiment, such a composition comprisesan effective concentration of a recombinant adeno-associated virus(rAAV) carrying a nucleic acid sequence encoding a CEP290 fragment ortruncated gene, as described herein, under the control of regulatorysequences which direct expression of the product of the gene in thesubject's ocular cells, formulated with a carrier and additionalcomponents suitable for injection. In still another embodiment, thetreatment methods are directed to ocular disorders and associatedconditions related thereto. Other treatment methods are also disclosed.

Unless defined otherwise, technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs and by reference to publishedtexts, which provide one skilled in the art with a general guide to manyof the terms used in the present application. The definitions usedherein are provided for clarity only and are not intended to limit theclaimed invention.

As used herein, the term “mammalian subject” or “subject” includes anymammal in need of these methods of treatment or prophylaxis, includingparticularly humans. Other mammals in need of such treatment orprophylaxis include dogs, cats, or other domesticated animals, horses,livestock, laboratory animals, including non-human primates, etc. Thesubject may be male or female. In another embodiment, the subject hasshown clinical signs of ciliopathy, such as Lebers Congenital Amaurosis.Clinical signs of LCA include, but are not limited to, decreasedperipheral vision, decreased central (reading) vision, decreased nightvision, loss of color perception, reduction in visual acuity, decreasedphotoreceptor function, pigmentary changes. In another embodiment, thesubject has been diagnosed with LCA. In yet another embodiment, thesubject has not yet shown clinical signs of LCA. In still anotherembodiment, the subject has shown signs or symptoms of anotherciliopathy, e.g., disorders of the bone, brain, CNS, kidney, orolefactory epithelia.

As used herein, the term “selected cells” refers to any cell in which aCEP290 mutation causes disease. In one embodiment, the selected cell isan ocular cell, which is any cell associated with the function of, theeye. In one embodiment, the ocular cell is a photoreceptor cells. Inanother embodiment, the term refers to rod, cone and photosensitiveganglion cells or retinal pigment epithelium (RPE) cells. In anotherembodiment, the selected cell is a bone cell. In another embodiment, theselected cell is a brain cell or neuron. In another embodiment, theselected cell is a renal or kidney cell. In another embodiment, theselected cell is a mucosal cell, such as an olfactory epithelial cell.

“CEP290 related pathologies” or those caused by a defect or mutation inCEP290 include Leber congenital amaurosis, Joubert syndrome, SeniorLoken Syndrome, and Meckel-Grüber syndrome, including isolated retinaldegeneration, renal dysfunction, central nervous system malformations,hepatic development defects, and embryonic lethality.

The terms “a” or “an” refers to one or more, for example, “a gene” isunderstood to represent one or more such genes. As such, the terms “a”(or “an”), “one or more,” and “at least one” are used interchangeablyherein. As used herein, the term “about” means a variability of 10% fromthe reference given, unless otherwise specified.

With regard to the following description, it is intended that each ofthe compositions herein described, is useful, in another embodiment, inthe methods of the invention. In addition, it is also intended that eachof the compositions herein described as useful in the methods, is, inanother embodiment, itself an embodiment of the invention. While variousembodiments in the specification are presented using “comprising”language, under other circumstances, a related embodiment is alsointended to be interpreted and described using “consisting of” or“consisting essentially of” language.

CEP290 Nucleic Acid and Proteins and Fragments Thereof

“CEP290” is a mammalian gene of about 7.8 kb in size (see NCBI databaseref gene 80184 for the full length human gene sequence) which encodes afull length protein of about 2479 amino acids (See e.g., SEQ ID NO: 1for the human gene sequence). CEP290 participates in the formation ofthe primary cilium (an organelle found in nearly all cell types) andregulates the trafficking of proteins into and out of the ciliarycompartment. Mutations in CEP290 lead to aberrant ciliary trafficking,eventually resulting in pathologies. Mutations in this gene have beenassociated with a variety of disease functions. It is implicated in LCA,as well as other ciliopathies affecting numerous organ systems,including the retina, CNS, kidney, liver heart and bone.

The nucleic acid sequence encoding a normal CEP290 gene may be derivedfrom any mammal which natively expresses the CEP290 gene, or homologthereof. In another embodiment, the CEP290 gene sequence is derived fromthe same mammal that the composition is intended to treat. In anotherembodiment, the CEP290 is derived from a human. In other embodiments,certain modifications are made to the CEP290 sequence in order toenhance the expression in the target cell. Such modifications includecodon optimization. Codon optimization may be performed in a manner suchas that described in, e.g., U.S. Pat. Nos. 7,561,972; 7,561,973; and7,888,112, incorporated herein by reference, and conversion of thesequence surrounding the translational start site to a consensus Kozaksequence. See, Kozak et al, Nucleic Acids Res. 15 (20): 8125-8148,incorporated herein by reference.

A full length human nucleic acid sequence for CEP290 is shown as SEQ IDNO. 1 and its full length protein sequence is shown as SEQ ID NO: 2. Afull length codon-optimized version of a human nucleic acid sequence isidentified herein as SEQ ID NO: 3 with its full length protein sequenceidentified as SEQ ID NO:4. Throughout this disclosure, numbering of theamino acid fragments of CEP is that of the amino acid sequence of FIG.10B, SEQ ID NO:2 with the first amino acid of FIG. 10B numbered as 1.

A “CEP290 fragment or truncation” as used herein is defined as afragment of CEP290 lacking the sequences that inhibit the protein'sfunction. By the term “fragment” or “functional fragment” is meant anyfragment that retains the function of the full length CEP290, althoughnot necessarily at the same level of expression or activity. Asdisclosed herein CEP290 is a microtubule binding protein, with its MTbinding activity localized to aa 1695 to 1966 of SEQ ID NO: 2, i.e., thesequence

DQSQKESQCLKSELQAQKEANSRAPTTTMRNLVERLKSQLALKEKQQKALSRALLELRAEMTAAAEERIISATSQKEAHLNVQQIVDRHTRELKTQVEDLNENLLKLKEALKTSKNRENSLTDNLNDLNNELQKKQKAYNKILREKEEIDQENDELKRQIKRLTSGLQGKPLTDNKQSLIEELQRKKKLENQLEGKVEEVDLKPMKEKNAKEELIRWEEGKKWQAKIEGIRNKLKEKEGEVFTLTKQLNTLKDLFAKADKEKLTLQRKLKT.

The inventors identified inhibitory regions at the N and C terminithereof. The inventors have also determined that the N- and C termini ofthe protein cooperatively inhibit the MT binding activity. As disclosedin detail in the examples below, the inventors determined that thenucleic acid sequence of CEP290 encoding amino acids spanning aa1695 to1966 were necessary for colocalization with microtubules. Whileinhibitory functions were found within the N terminal sequences encodingaa 1 to 580, other sequences located at the N-terminus were functionalin other ways, e.g., the sequences encoding amino acids 1 to 380 weredetermined to contain regions necessary for vesicular localization andamino acids 1 to 362 (SEQ ID NO: 45) were determined to contain regionsnecessary for membrane association. Amino acids 257 to 292 were found tobe the alpha helix and necessary for reversible interaction. TheC-terminal portions of the protein, from about amino acid 2000 to 2479(SEQ ID NO: 58) or about 1967 to 2479 (SEQ ID NO: 57), were found tocooperatively inhibit microtubule binding with portions of theN-terminal inhibitory sequence within amino acids 1 to 580.

CEP290 nucleic acid fragments or truncated sequences for use in thetherapeutic methods described herein can be a single consecutivesequence, such as that encoding CEP290 protein lacking its N terminalmembrane binding inhibitory region. In another embodiment, the nucleicacid sequence fragment encodes CEP290 lacking its C terminal membranebinding inhibitory region. In still another useful embodiment, thenucleic acid sequence fragment encodes CEP290 lacking both theN-terminal and C-terminal inhibitory regions. CEP290 fragments consistof a single consecutive CEP290 sequence or spliced together fragments ofone or more fragments of CEP290, which together provide the regionsnecessary for protein function. Such fragments can individually be fromabout 150 to over 1000 nucleotides in length. The encoded fragments canbe from about 50 to over 300 amino acids in length.

Thus in one embodiment a useful CEP209 nucleic acid sequence encodesaa1695 to about 2000 of CEP290 (SEQ ID NO: 56). In one embodiment, thenucleic acid sequence fragment encodes aa 1695 to aa 1990. In anotherembodiment, the sequence encodes aa 1695 to 1966. Still other nucleicacid sequences encoding continuous or discontinuous amino acidssequences within that range can be included as useful fragments herein.In another embodiment, a useful CEP290 fragment encodes aa100 to 362(SEQ ID NO: 48). In another embodiment the useful CEP290 fragmentencodes amino acids 130 to 380 of CEP290. In another embodiment theuseful CEP290 fragment encodes amino acids 130 to 380 of CEP290. Inanother embodiment the useful CEP290 fragment encodes amino acids 700 to1040 of CEP290. In another embodiment the useful CEP290 fragment encodesamino acids 1260 to 1605 of CEP290. In still another embodiment, splicedtogether fragments of one or more of the fragments of CEP290 disclosedherein provide the regions necessary for protein function. In anotherembodiment, to form a useful CEP290 fragment, the nucleic acid sequencesof CEP290 are spliced together in the same reading frame. In oneembodiment, the CEP290 fragment is useful for delivery to a mammaliancell to replace a mutated version of CEP290 is a nucleic acid minigeneencoding CEP fragments spliced together in a single reading frame: aa130to 380, aa 700 to 1040, aa 1260 to 1605, and aa1695 to 1990. Oneexemplary CEP290 minigene sequence is shown as SEQ ID NO: 5, with isencoded sequence being SEQ ID NO: 6.

In still another embodiment, the fragment of CEP290 is derived fromnucleic acid sequence SEQ ID NO: 1. In another embodiment, the fragmentof CEP290 is derived from human codon-optimized nucleic acid sequenceSEQ ID NO: 3. In still another embodiment the nucleic acid sequenceencoding a fragment of CEP290 is derived from or is the minigenesequence SEQ ID NO: 5. In one embodiment, the CEP290 fragment is usefulfor delivery to a mammalian cell to replace a mutated version.

It is anticipated that the CEP290 nucleic acid fragments and the CEP290protein truncates or amino acid fragments identified herein may toleratecertain minor modifications at the nucleic acid level to include, forexample, modifications to the nucleotide bases which are silent, e.g.,preference codons. In other embodiments, nucleic acid base modificationswhich change the amino acids, e.g. to improve expression of theresulting peptide/protein are anticipated. Also included as likelymodification of fragments are allelic variations, caused by the naturaldegeneracy of the genetic code. Also included as modification of theCEP290 expressed fragments are analogs, or modified versions, of theCEP290 protein fragments provided herein. Typically, such analogs differfrom the specifically identified CEP290 proteins by only one to fourcodon changes. Examples include CEP290 fragments with conservative aminoacid replacements from the CEP290 sequence from which the fragment isderived. Conservative replacements are those that take place within afamily of amino acids that are related in their side chains and chemicalproperties. CEP290 fragments which have at least 80% sequence identitywith the above derived fragments from known sequences of CEP290,including the SEQ ID NOs: 1 to 4 herein, are anticipated to be useful inthe compositions and methods of this invention.

The Vectors

A variety of known nucleic acid vectors may be used in these methods,e.g., recombinant viruses, such as recombinant adeno-associated virus(AAV), recombinant adenoviruses, recombinant retroviruses, recombinantpoxviruses, and other known viruses in the art, as well as plasmids,cosmids and phages, etc. A wealth of publications known to those ofskill in the art discusses the use of a variety of such vectors fordelivery of genes (see, e.g., Ausubel et al., Current Protocols inMolecular Biology, John Wiley & Sons, New York, 1989; Kay, M. A. et al,2001 Nat. Medic., 7(1):33 to 40; and Walther W. and Stein U., 2000Drugs, 60(2):249 to 71). In one embodiment of this invention the vectoris a recombinant AAV carrying a CEP290 fragment cDNA driven by apromoter that expresses the product of the CEP290 nucleic acid sequencein selected cells of the affected subject. Methods for assembly of therecombinant vectors are well-known (see, e.g., International PatentPublication No. WO 00/15822, published Mar. 23, 2000 and otherreferences cited herein). To exemplify the methods and compositions ofthis invention, the presently preferred vector, a recombinant AAV isdescribed in detail.

In certain embodiments of this invention, the CEP290 nucleic acidsequence, or fragment thereof, is delivered to the selected cells, e.g.,photoreceptor cells, in need of treatment by means of a viral vector, ofwhich many are known and available in the art. In certain embodiments,the therapeutic vector is desirably non-toxic, non-immunogenic, easy toproduce, and efficient in protecting and delivering DNA into the targetcells. In one particular embodiment, the viral vector is anadeno-associated virus vector.

More than 30 naturally occurring serotypes of AAV are available. Manynatural variants in the AAV capsid exist, allowing identification anduse of an AAV with properties specifically suited for ocular cells. AAVviruses may be engineered by conventional molecular biology techniques,making it possible to optimize these particles for cell specificdelivery of RPGR nucleic acid sequences, for minimizing immunogenicity,for tuning stability and particle lifetime, for efficient degradation,for accurate delivery to the nucleus, etc.

The expression of CEP290 functional nucleic acid fragments can beachieved in the selected cells through delivery by recombinantlyengineered AAVs or artificial AAV's that contain sequences encoding thedesired CEP290 fragment. The use of AAVs is a common mode of exogenousdelivery of DNA as it is relatively non-toxic, provides efficient genetransfer, and can be easily optimized for specific purposes. Among theserotypes of AAVs isolated from human or non-human primates (NHP) andwell characterized, human serotype 2 is the first AAV that was developedas a gene transfer vector; it has been widely used for efficient genetransfer experiments in different target tissues and animal models.Clinical trials of the experimental application of AAV2 based vectors tosome human disease models are in progress, and include such diseases ascystic fibrosis and hemophilia B. Other AAV serotypes include, but arenot limited to, AAV1, AAV3, AAV4, AAVS, AAV6, AAV7, AAV8 and AAV9. See,e.g., WO 2005/033321 for a discussion of various AAV serotypes, which isincorporated herein by reference. Still other modified AAV8 sequencesare described in U.S. patent application No. 61/762,775, filed Feb. 8,2013, incorporated by reference herein. For use in photoreceptor cells,a modified AAV 8_b is a useful vector, among others.

Desirable AAV fragments for assembly into vectors include the capproteins, including the vp1, vp2, vp3 and hypervariable regions, the repproteins, including rep 78, rep 68, rep 52, and rep 40, and thesequences encoding these proteins. These fragments may be readilyutilized in a variety of vector systems and host cells. Such fragmentsmay be used alone, in combination with other AAV serotype sequences orfragments, or in combination with elements from other AAV or non-AAVviral sequences. As used herein, artificial AAV serotypes include,without limitation, AAV with a non-naturally occurring capsid protein.Such an artificial capsid may be generated by any suitable technique,using a selected AAV sequence (e.g., a fragment of a vp1 capsid protein)in combination with heterologous sequences which may be obtained from adifferent selected AAV serotype, non-contiguous portions of the same AAVserotype, from a non-AAV viral source, or from a non-viral source. Anartificial AAV serotype may be, without limitation, a pseudotyped AAV, achimeric AAV capsid, a recombinant AAV capsid, or a “humanized” AAVcapsid. Pseudotyped vectors, wherein the capsid of one AAV is replacedwith a heterologous capsid protein, are useful in the invention. In oneembodiment, AAV2/5 a useful pseudotyped vector. In another preferredembodiment, the AAV is AAV2/8. See, Mussolino et al, cited above.

In one embodiment, the vectors useful in compositions and methodsdescribed herein contain, at a minimum, sequences encoding a selectedAAV serotype capsid, e.g., an AAV8 capsid, or a fragment thereof. Inanother embodiment, useful vectors contain, at a minimum, sequencesencoding a selected AAV serotype rep protein, e.g., AAV8 rep protein, ora fragment thereof. Optionally, such vectors may contain both AAV capand rep proteins. In vectors in which both AAV rep and cap are provided,the AAV rep and AAV cap sequences can both be of one serotype origin,e.g., all AAV8 origin. Alternatively, vectors may be used in which therep sequences are from an AAV serotype which differs from that which isproviding the cap sequences. In one embodiment, the rep and capsequences are expressed from separate sources (e.g., separate vectors,or a host cell and a vector). In another embodiment, these rep sequencesare fused in frame to cap sequences of a different AAV serotype to forma chimeric AAV vector, such as AAV2/8 described in U.S. Pat. No.7,282,199, which is incorporated by reference herein.

A suitable recombinant adeno-associated virus (AAV) is generated byculturing a host cell which contains a nucleic acid sequence encoding anadeno-associated virus (AAV) serotype capsid protein, or fragmentthereof, as defined herein; a functional rep gene; a minigene composedof, at a minimum, AAV inverted terminal repeats (ITRs) and a RPGRnucleic acid sequence; and sufficient helper functions to permitpackaging of the minigene into the AAV capsid protein. The componentsrequired to be cultured in the host cell to package an AAV minigene inan AAV capsid may be provided to the host cell in trans. Alternatively,any one or more of the required components (e.g., minigene, repsequences, cap sequences, and/or helper functions) may be provided by astable host cell which has been engineered to contain one or more of therequired components using methods known to those of skill in the art.

Most suitably, such a stable host cell will contain the requiredcomponent(s) under the control of an inducible promoter. The requiredcomponent(s) may be under the control of a constitutive promoter. Thepromoter of the host cell can also be the desired promoter for thevector used in the therapeutic compositions, and may depend upon theselected cell which is ultimately to be treated. Examples of suitableinducible and constitutive or cell/tissue specific promoters areprovided herein, in the discussion below of regulatory elements suitablefor use with the transgene, i.e., a functional fragment of CEP290. Instill another alternative, a selected stable host cell may containselected component(s) under the control of a constitutive promoter andother selected component(s) under the control of one or more induciblepromoters. For example, a stable host cell may be generated which isderived from 293 cells (which contain E1 helper functions under thecontrol of a constitutive promoter), but which contains the rep and/orcap proteins under the control of inducible promoters. Still otherstable host cells may be generated by one of skill in the art.

The minigene, rep sequences, cap sequences, and helper functionsrequired for producing the rAAV of the invention may be delivered to thepackaging host cell in the form of any genetic element which transfersthe sequences carried thereon. The selected genetic element may bedelivered by any suitable method, including those described herein. Themethods used to construct any embodiment of this invention are known tothose with skill in nucleic acid manipulation and include geneticengineering, recombinant engineering, and synthetic techniques. See,e.g., Sambrook et al, Molecular Cloning: A Laboratory Manual, ColdSpring Harbor Press, Cold Spring Harbor, N.Y. Similarly, methods ofgenerating rAAV virions are well known and the selection of a suitablemethod is not a limitation on the present invention. See, e.g., K.Fisher et al, 1993 J. Virol., 70:520 to 532 and U.S. Pat. No. 5,478,745,among others. These publications are incorporated by reference herein.

Unless otherwise specified, the AAV ITRs, and other selected AAVcomponents described herein, may be readily selected from among any AAVserotype, including, without limitation, AAV1, AAV2, AAV3, AAV4, AAVS,AAV6, AAV7, AAV8, AAV9 or other known and unknown AAV serotypes. TheseITRs or other AAV components may be readily isolated using techniquesavailable to those of skill in the art from an AAV serotype. Such AAVmay be isolated or obtained from academic, commercial, or public sources(e.g., the American Type Culture Collection, Manassas, Va.).Alternatively, the AAV sequences may be obtained through synthetic orother suitable means by reference to published sequences such as areavailable in the literature or in databases such as, e.g., GenBank,PubMed, or the like.

The desired AAV minigene is composed of, at a minimum, a CEP290functional fragment nucleic acid sequence (the transgene, e.g., such asthe fragment of SEQ ID NO: 5), as described herein, and its regulatorysequences, and 5′ and 3′ AAV inverted terminal repeats (ITRs). In oneembodiment, the ITRs of AAV serotype 2 are used. In another embodiment,the ITRs of AAV serotype 5 or 8 are used. However, ITRs from othersuitable serotypes may be selected. It is this minigene which ispackaged into a capsid protein and delivered to a selected host cell.

The Regulatory Sequences

The regulatory sequences include conventional control elements which areoperably linked to the CEP290 gene fragment or minigene in a mannerwhich permits its transcription, translation and/or expression in aselected cell transfected with the vector or infected with the virusproduced by the invention. As used herein, “operably linked” sequencesinclude both expression control sequences that are contiguous with thegene of interest and expression control sequences that act in trans orat a distance to control the gene of interest.

Expression control sequences include appropriate transcriptioninitiation, termination, promoter and enhancer sequences; efficient RNAprocessing signals such as splicing and polyadenylation (polyA) signals;sequences that stabilize cytoplasmic mRNA; sequences that enhancetranslation efficiency (i.e., Kozak consensus sequence); sequences thatenhance protein stability; and when desired, sequences that enhancesecretion of the encoded product. A great number of expression controlsequences, including promoters, are known in the art and may beutilized.

The regulatory sequences useful in the constructs of the presentinvention may also contain an intron, desirably located between thepromoter/enhancer sequence and the gene. One desirable intron sequenceis derived from SV to 40, and is a 100 bp mini-intron splicedonor/splice acceptor referred to as SD-SA. Another suitable sequenceincludes the woodchuck hepatitis virus post-transcriptional element.(See, e.g., L. Wang and I. Verma, 1999 Proc. Natl. Acad. Sci., USA,96:3906 to 3910). PolyA signals may be derived from many suitablespecies, including, without limitation SV-40, human and bovine.

Another regulatory component of the rAAV useful in the method of theinvention is an internal ribosome entry site (IRES). An IRES sequence,or other suitable systems, may be used to produce more than onepolypeptide from a single gene transcript. An IRES (or other suitablesequence) is used to produce a protein that contains more than onepolypeptide chain or to express two different proteins from or withinthe same cell. An exemplary IRES is the poliovirus internal ribosomeentry sequence, which supports transgene expression in photoreceptors,RPE and ganglion cells. Preferably, the IRES is located 3′ to thetransgene in the rAAV vector.

The selection of the promoter to be employed in the rAAV may be madefrom among a wide number of constitutive or inducible promoters that canexpress the CIP290 functional fragment transgene in the selected cell.In another embodiment, the promoter is cell-specific. The term“cell-specific” means that the particular promoter selected for therecombinant vector can direct expression of the selected transgene in aparticular cell type.

In an embodiment in which the selected cell is a mammalianphotoreceptor, the regulatory sequence comprises a promoter thatexpresses the product of the CEP290 fragment in mammalianphotoreceptors. In one embodiment, the promoter is specific forexpression of the transgene in photoreceptor cells. In anotherembodiment, the promoter is specific for expression in the rods andcones. In another embodiment, the promoter is specific for expression inthe rods. In another embodiment, the promoter is specific for expressionin the cones. In another embodiment, the promoter is specific forexpression of the transgene in RPE cells. In another embodiment, whereinthe selected cells is a mammalian cell is a kidney cell, brain cell orolfactory epithelium.

Suitable promoters for expression in photoreceptors may be selected fromthe rhodopsin promoter, the rhodopsin kinase promoter (51), the RPGTPaseregulator (RPGR) promoter, the IRBP promoter, the GRK1 promoter.Alternatively, the promoter may be a constitutive promoter such as achicken beta actin promoter, a chicken beta actin promoter with acytomegalovirus enhancer, or modifications thereof, such as modificationto shorten the length of the promoter.

In an embodiment in which the selected cell is a mammalian kidney cell,the regulatory sequence comprises a promoter that expresses the productof the CEP290 fragment in mammalian kidney cells. In an embodiment inwhich the selected cell is a mammalian brain cell or neuron of the CNS,the regulatory sequence comprises a promoter that expresses the productof the CEP290 fragment in mammalian CNS or brain cells. In an embodimentin which the selected cell is a mammalian bone cell, the regulatorysequence comprises a promoter that expresses the product of the CEP290fragment in mammalian bone cells. In an embodiment in which the selectedcell is a mammalian mucosal epithelial cell, such as olfactoryepithelial cells, the regulatory sequence comprises a promoter thatexpresses the product of the CEP290 fragment in mammalian epithelialcells. Still other cellular targets suitable for expression of theCEP290 nucleic acid functional fragments may direct selection of thepromoter.

The promoter may be derived from any species. In another embodiment, thepromoter is the human G-protein-coupled receptor protein kinase 1 (GRK1)promoter (Genbank Accession number AY327580). In another embodiment, thepromoter is a 292 nt fragment (positions 1793 to 2087) of the GRK1promoter (See also, Beltran et al, Gene Therapy 2010 17:1162-74, whichis hereby incorporated by reference herein). In another preferredembodiment, the promoter is the human interphotoreceptorretinoid-binding protein proximal (IRBP) promoter. In one embodiment,the promoter is a 235 nt fragment of the hIRBP promoter. In anotherembodiment, promoter is the native promoter for the gene to beexpressed. In one embodiment, the promoter is the RPGR proximal promoter(Shu et al, IOVS, May 2012, which is incorporated by reference herein).Other promoters useful in the invention include, without limitation, therod opsin promoter, the red-green opsin promoter, the blue opsinpromoter, the cGMP-β-phosphodiesterase promoter, the mouse opsinpromoter (Beltran et al 2010 cited above), the rhodopsin promoter(Mussolino et al, Gene Ther, July 2011, 18(7):637 to 45); thealpha-subunit of cone transducin (Morrissey et al, BMC Dev, Biol,January 2011, 11:3); beta phosphodiesterase (PDE) promoter; theretinitis pigmentosa (RP1) promoter (Nicord et al, J. Gene Med, December2007, 9(12):1015-23); the NXNL2/NXNL1 promoter (Lambard et al, PLoS One,October 2010, 5(10):e13025), the RPE65 promoter; the retinaldegeneration slow/peripherin 2 (Rds/perph2) promoter (Cai et al, Exp EyeRes. 2010 August; 91(2):186-94); and the VMD2 promoter (Kachi et al,Human Gene Therapy, 2009 (20:31-39)). Each of these documents isincorporated by reference herein. In one embodiment, the promoter is ofa small size, under 1000 bp, due to the size limitations of the AAVvector. In another embodiment, the promoter is under 400 bp.

Examples of constitutive promoters useful in the invention include,without limitation, the retroviral Rous sarcoma virus (RSV) LTR promoter(optionally with the RSV enhancer), the cytomegalovirus (CMV) promoter(optionally with the CMV enhancer), the SV40 promoter, the dihydrofolatereductase promoter, the chicken β-actin (CBA) promoter, thephosphoglycerol kinase (PGK) promoter, the EF1 promoter (Invitrogen),and the immediate early CMV enhancer coupled with the CBA promoter(Beltran et al, Gene Therapy 2010 cited above).

Inducible promoters allow regulation of gene expression and can beregulated by exogenously supplied compounds, environmental factors suchas temperature, or the presence of a specific physiological state, e.g.,acute phase, a particular differentiation state of the cell, or inreplicating cells only. Inducible promoters and inducible systems areavailable from a variety of commercial sources, including, withoutlimitation, Invitrogen, Clontech and Ariad. Many other systems have beendescribed and can be readily selected by one of skill in the art.Examples of inducible promoters regulated by exogenously suppliedcompounds, include, the zinc-inducible sheep metallothionine (MT)promoter, the dexamethasone (Dex)-inducible mouse mammary tumor virus(MMTV) promoter, the T7 polymerase promoter system; the ecdysone insectpromoter, the tetracycline-repressible system, thetetracycline-inducible system, the RU486-inducible system and therapamycin-inducible system. Other types of inducible promoters which maybe useful in this context are those which are regulated by a specificphysiological state, e.g., temperature, acute phase, a particulardifferentiation state of the cell, or in replicating cells only. Anytype of inducible promoter which is tightly regulated and is specificfor the particular target ocular cell type may be used.

Other regulatory sequences useful in the invention include enhancersequences. Enhancer sequences useful in the invention include the IRBPenhancer (Nicord 2007, cited above), immediate early cytomegalovirusenhancer, one derived from an immunoglobulin gene or SV40 enhancer, thecis-acting element identified in the mouse proximal promoter, etc.

Selection of these and other common vector and regulatory elements areconventional and many such sequences are available. See, e.g., Sambrooket al, and references cited therein at, for example, pages 3.18 to 3.26and 16.17 to 16.27 and Ausubel et al., Current Protocols in MolecularBiology, John Wiley & Sons, New York, 1989). Of course, not all vectorsand expression control sequences will function equally well to expressall of the transgenes of this invention. However, one of skill in theart may make a selection among these, and other, expression controlsequences without departing from the scope of this invention.

The Pharmaceutical Carrier and Pharmaceutical Compositions

The compositions of the present invention containing the recombinantviral vector, e.g., AAV, containing the desired transgene andcell-specific promoter for use in the selected target cells, e.g.,photoreceptor cells for treatment of LCA, as detailed above ispreferably assessed for contamination by conventional methods and thenformulated into a pharmaceutical composition intended for a suitableroute of administration. Still other compositions containing the desiredCEP290 fragment, e.g., naked DNA or as protein, may be formulatedsimilarly with a suitable carrier. Such formulation involves the use ofa pharmaceutically and/or physiologically acceptable vehicle or carrier,particularly directed for administration to the target cell. In oneembodiment, carriers suitable for administration to the photoreceptorcells of the eye include buffered saline, an isotonic sodium chloridesolution, or other buffers, e.g., HEPES, to maintain pH at appropriatephysiological levels, and, optionally, other medicinal agents,pharmaceutical agents, stabilizing agents, buffers, carriers, adjuvants,diluents, etc.

For injection, the carrier will typically be a liquid. Exemplaryphysiologically acceptable carriers include sterile, pyrogen-free waterand sterile, pyrogen-free, phosphate buffered saline. A variety of suchknown carriers are provided in U.S. Pat. No. 7,629,322, incorporatedherein by reference. In one embodiment, the carrier is an isotonicsodium chloride solution. In another embodiment, the carrier is balancedsalt solution. In one embodiment, the carrier includes tween. If thevirus is to be stored long-term, it may be frozen in the presence ofglycerol or Tween20.

In other embodiments, e.g., compositions containing the CEP290 proteinor amino acid, e.g., the single reading frame protein of SEQ ID NO: 6,the pharmaceutical compositions include a surfactant. Usefulsurfactants, such as Pluronic F68 ((Poloxamer 188), also known asLutrol® F68) may be included with the vectored CEP290 as they preventAAV from sticking to inert surfaces and thus ensure delivery of thedesired dose.

As an example, one illustrative composition designed for the treatmentof LCA comprises a recombinant adeno-associated vector carrying anucleic acid sequence encoding a fragment of the CEP290 gene lacking atleast one of its N-terminal and C-terminal inhibitory regions, under thecontrol of regulatory sequences which express the product of said genein a photoreceptor cell of a mammalian subject, and a pharmaceuticallyacceptable carrier. In one embodiment, the AAV is AAV8b. In anotherembodiment, the AAV is AAV 2/5. In another embodiment, the CEP290nucleic acid fragment is any of the fragments described above or one ormore of the fragments spliced together or otherwise administeredtogether. One such combination is the minigene of SEQ ID NO: 5. Thecarrier is isotonic sodium chloride solution and includes a surfactantPluronic F68.

In yet another exemplary embodiment, the composition comprises arecombinant AAV2/5 pseudotyped adeno-associated virus carrying a nucleicacid sequence encoding aa 1695 to 1965 of CEP290, the nucleic acidsequence under the control of a rhodopsin kinase promoter which directsexpression of the product of said gene in said photoreceptor cells,wherein the composition is formulated with a carrier and additionalcomponents suitable for subretinal injection.

In yet another exemplary embodiment, the composition comprises simplyunvectored naked minigene CEP290 or other fragments or spliced variantof CEP290 having the functions of natural or wildtype CEP290 formulatedwith a carrier.

Methods of Treatment/Prophylaxis

The compositions described above are useful in methods of treating amammalian subject having a disease associated with a CEP290 mutation.These methods comprise administering to a subject in need thereofsubject an effective concentration of a composition of any of thosedescribed herein.

In one illustrative embodiment, such a method is provided forpreventing, arresting progression of or ameliorating vision lossassociated with Lebers Congenital Amaurosis in a subject, said methodcomprising administering to a mammalian subject in need thereof aneffective concentration of a composition comprising a recombinantadeno-associated virus (AAV) carrying a nucleic acid sequence encoding afragment of the CEP290 gene lacking at least one of its N-terminal andC-terminal inhibitory regions, under the control of regulatory sequenceswhich express the product of said gene in a photoreceptor cell of amammalian subject, and a pharmaceutically acceptable carrier.

By “administering” as used in the methods means delivering thecomposition to the target selected cell based on the disease caused byCEP290 mutation or defect, and on the selected cell. For example, in oneembodiment, the method involves delivering the composition by subretinalinjection to the photoreceptor cells or other ocular cells. In anotherembodiment, intravitreal injection to ocular cells or injection via thepalpebral vein to ocular cells may be employed. In another embodiment,the method involves delivering the composition via retrograde urethralinjection to the kidney. In still another embodiment, the methodinvolves delivering the composition by intra-ventricular orintra-cerebral injection to the brain. In yet a further embodiment, themethod involves topically delivering the composition to nasalepithelium. Still other methods of administration may be selected by oneof skill in the art given this disclosure.

Furthermore, in certain embodiments of the invention it is desirable toperform non-invasive retinal imaging and functional studies to identifyareas of retained photoreceptors to be targeted for therapy. In theseembodiments, clinical diagnostic tests are employed to determine theprecise location(s) for one or more subretinal injection(s). These testsmay include electroretinography (ERG), perimetry, topographical mappingof the layers of the retina and measurement of the thickness of itslayers by means of confocal scanning laser ophthalmoscopy (cSLO) andoptical coherence tomography (OCT), topographical mapping of conedensity via adaptive optics (AO), functional eye exam, etc. In view ofthe imaging and functional studies, in some embodiments of the inventionone or more injections are performed in the same eye in order to targetdifferent areas of retained photoreceptors.

For use in these methods, the volume and viral titer of each injectionis determined individually, as further described below, and may be thesame or different from other injections performed in the same, orcontralateral, eye, where the disease is LCA. In another embodiment, asingle, larger volume injection is made in order to treat the entireeye. Where the diseases are related to CEP290 expression or defect inanother organ, the dosages, administrations and regimens may bedetermined by the attending physician given the teachings of thisspecification.

In one embodiment, the volume and concentration of the rAAV compositionis selected so that only the certain regions of photoreceptors isimpacted. In another embodiment, the volume and/or concentration of therAAV composition is a greater amount, in order reach larger portions ofthe eye. Similarly dosages are adjusted for administration to otherorgans.

An effective concentration of a recombinant adeno-associated viruscarrying a nucleic acid sequence encoding the CEP290 nucleic acidfunctional fragment or minigene under the control of the selectedpromoter sequence ranges between about 10⁸ and 10¹³ vector genomes permilliliter (vg/mL). The rAAV infectious units are measured as describedin S. K. McLaughlin et al, 1988 J. Virol., 62:1963. In anotherembodiment, the concentration ranges between 10⁹ and 10¹³ vector genomesper milliliter (vg/mL). In another embodiment, the effectiveconcentration is about 1.5×10¹¹ vg/mL. In one embodiment, the effectiveconcentration is about 1.5×10¹⁰ vg/mL. In another embodiment, theeffective concentration is about 2.8×10¹¹ vg/mL. In yet anotherembodiment, the effective concentration is about 1.5×10¹² vg/mL. Inanother embodiment, the effective concentration is about 1.5×10¹³ vg/mL.It is desirable that the lowest effective concentration of virus beutilized in order to reduce the risk of undesirable effects, such astoxicity, and other issues related to administration to the eye, e.g.,retinal dysplasia and detachment. Still other dosages in these ranges orin other units may be selected by the attending physician, taking intoaccount the physical state of the subject, preferably human, beingtreated, including the age of the subject; the composition beingadministered, e.g., viral vector, AAV, naked DNA or protein-containing;and the particular CEP-290-related disorder, e.g., LCA, Joubertsyndrome, Senior Loken Syndrome, or Meckel-Grüher syndrome; the targetedcell or organ type, and the degree to which the disorder, ifprogressive, has developed.

The composition may be delivered in a volume of from about 50 μL toabout 1 mL, including all numbers within the range, depending on thesize of the area to be treated, the viral titer used, the route ofadministration, and the desired effect of the method. In one embodiment,the volume is about 50 μL. In another embodiment, the volume is about 70μL. In another embodiment, the volume is about 100 μL. In anotherembodiment, the volume is about 125 μL. In another embodiment, thevolume is about 150 μL. In another embodiment, the volume is about 175μL. In yet another embodiment, the volume is about 200 μL. In anotherembodiment, the volume is about 250 μL. In another embodiment, thevolume is about 300 μL. In another embodiment, the volume is about 450μL. In another embodiment, the volume is about 500 μL. In anotherembodiment, the volume is about 600 μL. In another embodiment, thevolume is about 750 μL. In another embodiment, the volume is about 850μL. In another embodiment, the volume is about 1000 μL.

The invention provides various methods of preventing, treating,arresting progression of or ameliorating the CEP290-related diseases ordisorders, exemplified by LCA, including ocular diseases and retinalchanges associated therewith. Such treatment can treat or prevent theadvanced of loss of photoreceptor structure or function and blindnessassociated with LCA caused by a defect in CEP290. The expression of thefunctional fragment of CEP290 in the targeted cell can result inimprovement of the subject's vision or an arrest of vision loss.

In another embodiment, the invention provides a method to prevent, orarrest photoreceptor function loss, or increase photoreceptor functionin the subject. Photoreceptor function may be assessed using thefunctional studies described herein, e.g., ERG or perimetry, which areconventional in the art. As used herein “photoreceptor function loss”means a decrease in photoreceptor function as compared to a normal,non-diseased eye or the same eye at an earlier time point. As usedherein, “increase photoreceptor function” means to improve the functionof the photoreceptors or increase the number or percentage of functionalphotoreceptors as compared to a diseased eye (having the same oculardisease), the same eye at an earlier time point, a non-treated portionof the same eye, or the contralateral eye of the same patient.

For each of the described methods, the treatment may be used to preventthe occurrence of further damage or to rescue tissues or organ, e.g.,eyes in a subject with LCA, having mild or advanced disease. As usedherein, the term “rescue” means to prevent progression of the disease,e.g., to total blindness with LCA, prevent spread of damage to uninjuredphotoreceptor cells or to improve damage in injured photoreceptor cells.

Thus, in one embodiment, the composition is administered before diseaseonset. In another embodiment, the composition is administered prior tothe initiation of photoreceptor loss. In another embodiment, thecomposition is administered after initiation of photoreceptor loss. Inyet another embodiment, the composition is administered when less than90% of the photoreceptors are functioning or remaining, as compared to anon-diseased eye.

In another embodiment of the invention, the method includes performingfunctional and imaging studies to determine the efficacy of thetreatment. These studies include ERG and in vivo retinal imaging, asdescribed in U.S. Pat. No. 8,147,823; in US patent application No.61/670,355 or 61/762,775, incorporated by reference. In addition visualfield studies, perimetry and microperimetry, mobility testing, visualacuity, color vision testing may be performed.

In yet another embodiment of the invention, any of the above describedmethods is performed in combination with another, or secondary, therapy.The therapy may be any now known, or as yet unknown, therapy which helpsprevent, arrest or ameliorate CEP290 mutations or defects or any of theeffects associated therewith. The secondary therapy can be administeredbefore, concurrent with, or after administration of the rAAV describedabove.

EXAMPLES

The examples below present evidence that CEP290 directly binds to theciliary membrane through a highly conserved region in its N-terminus andto microtubules through a domain located near its C terminus. CEP290activity was found to be regulated by autoinhibitory domains locatedwithin its N and C-termini, both of which were found to play a criticalrole in regulating ciliogenesis. Furthermore, the inventors determinedthat the microtubule-binding domain is completely disrupted in the rd16mouse LCA model (17), resulting in significant deficits in ciliumformation leading to retinal degeneration.

These findings implicate CEP290 both as a key structural component ofthe ciliary Y-links and as a terminal regulator in the pathway leadingto ciliogenesis. This data provides the first evidence of a mechanisticand pathological basis for CEP290-related LCA and related ciliopathiesand supports novel therapeutic methods. Restoration of cellular functionby the method of this invention can be assessed in an animal model ofthe appropriate disease caused by CEP290 defect or mutation, such as therestoration of visual function in a subject with a CEP290 defect causingLCA in the rd16 mouse LCA model or canine model of LCA. The use of theexemplary vector can demonstrate that the defect in the mutant dog orother animal model could be corrected by gene delivery. This data allowone of skill in the art to readily anticipate that this method may besimilarly used in treatment of XLRP or other types of retinal disease inother subjects, including humans.

Example 1—Materials and Methods Plasmid Construction

CEP290 truncations were generated by PCR amplification using Gateway®cloning (Invitrogen) compatible primers identified below in Table 1 froma human codon-optimized CEP290 plasmid synthesized by DNA 2.0. Amplifiedproducts were directly cloned into pDONR221 (Invitrogen) by Gateway®cloning to generate entry clones. For cell transfection and in vitrotranscription and translation assays, entry clones were shuttled intothe plasmid pcDNA-DEST53 (Invitrogen) by Gateway® LR clonase reactionsto create N-terminally tagged GFP fusions.

TABLE 1 primers used to generate truncation mutants Trun- SEQ cationID NO. Primer Sequence aa 1- 7 ForwardGGGGACAAGTTTGTACAAAAAAGCAGGCTTCGAAGG 2479AGATAGAACCATGCCCCCAAACATCAATTGG 8 ReverseGGGGACCACTTTGTACAAGAAAGCTGGGTCCTAATA GATCGGGAAGTTAACAGG aa 9 ForwardGGGGACAAGTTTGTACAAAAAAGCAGGCTTCGAAGG 580 to 2479AGATAGAACCATGACGGAGAACATAAGCCAAGG 10 ReverseGGGGACCACTTTGTACAAGAAAGCTGGGTCCTAATA GATCGGGAAGTTAACAGG aa 1 to 580 11Forward GGGGACAAGTTTGTACAAAAAAGCAGGCTTCGAAGGAGATAGAACCATGCCCCCAAACATCAATTGG 12 ReverseGGGGACCACTTTGTACAAGAAAGCTGGGTCCTAAAG ATTCAGATCCTCGGTAG aa 1-362 13Forward GGGGACAAGTTTGTACAAAAAAGCAGGCTTCGAAGGAGATAGAACCATGCCCCCAAACATCAATTGG 14 ReverseGGGGACCACTTTGTACAAGAAAGCTGGGTCCTAATC CCTTTCTTGGATTCCCTGC aa 380- 15Forward GGGGACAAGTTTGTACAAAAAAGCAGGCTTCGAAGG 580AGATAGAACCATGAAAAACACTTGCATCATTGAGGA C 16 ReverseGGGGACCACTTTGTACAAGAAAGCTGGGTCCTAAAG ATTCAGATCCTCGGTAG aa 1- 17 ForwardGGGGACAAGTTTGTACAAAAAAGCAGGCTTCGAAGG 1695AGATAGAACCATGCCCCCAAACATCAATTGG 18 ReverseGGGGACCACTTTGTACAAGAAAGCTGGGTCCTAATC CAGCAGATACTTCAAATCC aa 580- 19Forward GGGGACAAGTTTGTACAAAAAAGCAGGCTTCGAAGG 1695AGATAGAACCATGACGGAGAACATAAGCCAAGG 20 ReverseGGGGACCACTTTGTACAAGAAAGCTGGGTCCTAATC CAGCAGATACTTCAAATCC aa 1- 21Forward GGGGACAAGTTTGTACAAAAAAGCAGGCTTCGAAGG 1966AGATAGAACCATGCCCCCAAACATCAATTGG 22 ReverseGGGGACCACTTTGTACAAGAAAGCTGGGTCCTATGT TTTCAGCTTTCTCTGCAG aa 580- 23Forward GGGGACAAGTTTGTACAAAAAAGCAGGCTTCGAAGG 2479AGATAGAACCATGACGGAGAACATAAGCCAAGG 24 ReverseGGGGACCACTTTGTACAAGAAAGCTGGGTCCTAATA GATCGGGAAGTTAACAGG aa 580- 25Forward GGGGACAAGTTTGTACAAAAAAGCAGGCTTCGAAGG 1966AGATAGAACCATGACGGAGAACATAAGCCAAGG 26 ReverseGGGGACCACTTTGTACAAGAAAGCTGGGTCCTATGT TTTCAGCTTTCTCTGCAG aa 1695- 27Forward GGGGACAAGTTTGTACAAAAAAGCAGGCTTCGAAGG 1966AGATAGAACCATGCAGTCCCAGAAGGAGTCAC 28 ReverseGGGGACCACTTTGTACAAGAAAGCTGGGTCCTATGT TTTCAGCTTTCTCTGCAG aa 1966- 29Forward GGGGACAAGTTTGTACAAAAAAGCAGGCTTCGAAGG 2479AGATAGAACCATGACAGGCATGACCGTGGAC 30 ReverseGGGGACCACTTTGTACAAGAAAGCTGGGTCCTAATA GATCGGGAAGTTAACAGG aa 1695- 31Forward GGGGACAAGTTTGTACAAAAAAGCAGGCTTCGAAGG 1903AGATAGAACCATGCAGTCCCAGAAGGAGTCAC 32 ReverseGGGGACCACTTTGTACAAGAAAGCTGGGTCCTATTTC TCTTTCATGGGCTTAAGGTC aa 1903- 33Forward GGGGACAAGTTTGTACAAAAAAGCAGGCTTCGAAGG 2479AGATAGAACCATGACAGGCATGACCGTGGACC 34 ReverseGGGGACCACTTTGTACAAGAAAGCTGGGTCCTAATA GATCGGGAAGTTAACAGG

For bacterial expression, entry clones were shuttled into pDest-527 (agift of Dominic Esposito (Addgene plasmid #11518)) to createN-terminally-tagged 6×His fusions. For lentivirus production, entryclones were shuttled into pLXnGFP, a modified version of pLX302 (a giftof David Root (Addgene plasmid #25896)), to create N-terminally-taggedGFP fusion lentivirus production plasmids. pLXnGFP was created by thereplacement of the gateway cassette of pLX302 with an eGFP cassettecontaining an EcoRV site just downstream of the eGFP ORF by BsrGIdigestion and ligation. The Gateway A cassette was then inserted intothe EcoRV site using the Gateway Conversion Kit (Invitrogen).Restriction digest and DNA sequencing were used to confirm the integrityof each expression construct.

shRNA constructs were created as follows. Three regions of the humanCEP290 coding sequence without homology to other transcripts wereselected as shRNA targets. Oligonucleotides encoding the target sequencein the context of a DNA hairpin were synthesized, annealed, and ligatedinto the pSIREN-RetroQ retrovirus vector (Clontech). Efficiency ofknockdown was assayed. The mammalian expression vector encodingGFP-fused miniCEP290 was created by the amplification of the miniCEP290gene by PCR using primers compatible with Gateway® cloning (Invitrogen).Amplified products were cloned into pDONR221 (Invitrogen) by Gateway®cloning to generate entry clones and subsequently shuttled into theplasmid pcDNA-DEST53 (Invitrogen) by Gateway® LR clonase reactions tocreate N-terminally-tagged GFP fusions.

miniCEP290 Synthesis

The miniCEP290 construct was codon optimized, synthesized, and sequencedby DNA2.0.

Cell Culture and Treatments; Lentivirus Production; RetrovirusProduction

Wild type and rd16 mouse primary dermal fibroblasts and human 293T cellswere grown in DMEM supplemented with 10% FBS. hTERT RPE to 1 cells weregrown in DMEM:F12 supplemented with 10% FBS and 0.075% sodiumbicarbonate. All cells were grown at 37° C. in a humidified 5% CO₂atmosphere. All transfections were performed with FuGENE 6 reagent(Promega) according to the manufacturer's protocol. Cells were inducedto form primary cilia by serum starvation with OptitoMEM I (Invitrogen)for 48 to 72 hours.

Lentiviral vectors were produced by transfection of 80% confluent 293Tcells grown in T25 culture flasks with 1 μg of lentivirus construct, 750ng of PsPAX2 packaging plasmid, and 250 ng of pMD2.G envelope plasmidusing FuGENE6. Media was replaced after 24 hours, and lentiviralsupernatants were harvested at 48 and 72 hours after transfection,combined, filtered through a 0.45 μm filter, and snap-frozen at to 80°C. For lentivirus transduction, hTERT RPE-1 cells were plated in 6 wellplates in media containing 8 μg/mL polybrene. 0.5 mL of filtered mediacontaining the appropriate lentivirus particles was added to each well.24 hours after transduction cells were switched to media containing 10μg/mL puromycin and maintained in selective media from that point on.All experiments carried out on lentivirus transduced cells wereperformed 10 days post transduction.

Retroviral vectors were produced by transfection of 80% confluent 293Tcells in 100 mm culture dishes with 10 μg of retrovirus construct and 10μg of pCL10A1 packaging plasmid. Media was replaced after 24 hours, andretroviral supernatants were harvested at 48 and 72 hours, combined,filtered through a 0.45 μm filter, and snap-frozen at −80° C. Forretrovirus transduction, hTERT RPE-1 cells were plated in mediacontaining 8 μg/mL polybrene. Filtered media containing the appropriateretroviral particles was added and 24 hours after transduction cellswere switched to selective media containing 10 μg/mL puromycin.

Primary Dermal Fibroblast Isolation

Primary dermal fibroblasts were isolated by washing sections of neonatalmouse skin in 70% ethanol followed by 5 washes in PBS. The skin wasminced and applied to the bottom of a culture vessel, covered with DMEMsupplemented with 10% FBS, penicillin, and streptomycin, and incubatedat 37° C. in a humidified 5% CO₂ atmosphere. One week after harvestingthe skin was removed and discarded and fibroblasts were passaged into alarger vessel.

Antibodies, Immunofluorescence, and Immunoblotting

Antibodies used in this study were rabbit anti-human CEP290 (Abcam,ab105383), rabbit anti-mouse Cep290 (Abcam, ab128231), mouse anti-αtubulin (Abcam, AB7291), rabbit anti-pericentrin (Abcam, AB4448), mouseanti-GFP (Roche 11 814 460 001), mouse anti-Bovine serum albumin(Thermo, MA5 to 15238), rabbit anti-6×His (Abcam, AB1187), rabbitanti-GAPDH (Sigma, SAB2103104), mouse anti-Na/K ATPase α-1 (Novus, NB300to 146), mouse anti-Lamin A/C (Sigma, SAB4200236), mouse anti-Acetylatedα-tubulin (Sigma, T7451), rabbit anti-LAMP2 (Novus, NBP1 to 71692),rabbit anti-Annexin A2 (Cell Signaling, 8235), rabbit anti-ARL13B(Proteintech, 17711-1-AP), HRP-conjugated goat anti-mouse (GE, NA931V),HRP-conjugated goat anti-rabbit (GE, NA934V), Cy5 conjugated goatanti-rabbit (KPL, 072-02-15-06), and AlexaFluor 594-conjugated goatanti-mouse (Invitrogen, A1100S).

For immunofluorescence, cells were grown in chamber slides and fixedwith 3% PFA in PBS for 20 minutes at 37° C. Cells were permeabilizedwith 1% Triton X-100 in PBS for 5 minutes, and blocked in 2% BSA in PBSfor 30 minutes prior to incubation with primary antibody. Secondaryantibodies used were donkey anti-mouse or anti-rabbit, conjugated to Cy5or AlexaFluor 594. Slides were mounted in mounting medium containingDAPI. Confocal imaging was performed with an LSM510 META NLO laserscanning confocal on a Zeiss Axiovert 200M inverted microscope using aPlan-Apo 63×/1.4 oil objective and the LSM510 4.2 software. Laser linesused were 488 nm (for green labeling, from argon laser), 543 nm (for redlabeling, HeNe laser), 633 nm (for Cy5 channel, HeNe laser), and 740 nm(for DAPI channel, from a Coherent Chameleon tunable two photon laser).For normal fluorescence microscopy, slides were imaged using an AxioImager.M2 microscope using an either EC Plan-Neofluar 40×/0.75 M27 or anEC Plan-Neofluar 63×/1.25 Oil M27 objective and captured using anAxioCamMR3 camera and the AxioVs40 software, version 4.8.2.0. Primarycilium length was measured using the same AxioVs40 software.

For immunoblotting, samples were subjected to SDS-PAGE and transferredto nitrocellulose membrane using standard techniques. Membranes wereblocked in 5% nonfat milk for 1 hour at room temperature andsubsequently incubated in primary antibody overnight at 4° C. Membraneswere washed three times with PBST (0.1% TweeN-20 in PBS) and incubatedwith HRP-conjugated secondary antibody for 1 hour at room temperature.Membranes were washed three times with PBST, developed using ECL2reagent (Pierce), and scanned on a Typhoon 9400 instrument (GE).Immunoblots were quantified by densitometry using ImageJ 1.44p.

Membrane Flotation, Membrane Protein Fractionation, and VesicleImmunoprecipitation

Cultured cells were washed three times with ice cold PBS. Cells werethen resuspended in a 250 mM Sucrose solution containing 4 mM Immidazoleand a protease inhibitor cocktail and passaged through a 25G needle 20times to rupture the plasma membrane. The resulting lysate wascentrifuged at 1,000×g for 10 minutes at 4° C. to pellet nuclei andunlysed cells and the resulting post-nuclear supernatant was centrifugedat 100,000×g for 60 minutes at 4° C. to pellet the membrane-enrichedfraction. Membrane flotation was performed by resuspending themembrane-enriched fraction in 250 μL of 80% sucrose in PBS. Thissolution was added to the bottom of a 2 mL centrifuge tube, overlaidwith 1.5 mL of 50% sucrose in PBS, and in turn overlaid with 250 μL of5% sucrose in PBS. Sucrose gradients were centrifuged at 100,000×g for16 hours at 4° C. to induce the membrane and membrane associatedproteins to float to the top of the gradient. Equal fractions weresubsequently taken from the top to the bottom of the gradient andanalyzed by western blotting as indicated. Peripheral membrane proteinswere extracted from membrane preparations by resuspending and incubatingthe membrane-enriched fraction of cultured cells in a high pH buffer(100 nM Na2CO3, pH 11.3) for 30 minutes at 4° C. The remaining membraneswere pelleted at 100,000×g for 60 minutes at 4° C. and the resultingsupernatant was saved as the peripheral membrane fraction. Integralmembrane proteins were subsequently extracted by resuspending andincubating the resulting membrane pellet in 4% TritoN-X100 in PBS for 30minutes at 4° C. Both fractions were analyzed by immunoblotting for theCEP290 truncations being tested and for the indicated fractionationcontrols. Vesicle immunoprecipitation was performed on post-nuclearsupernatants of hTERT-RPE1 cells expressing various CEP290 truncations.

A sample of the total post nuclear extract was saved as the inputfraction. Protein G Dynabeads (Invitrogen) were washed and incubatedwith 2 μg of anti-ARL13B antibody for 20 minutes at room temperature,magnetically collected, and washed three times with PBS. 350 μL ofpost-nuclear supernatant was added to the antibody-dynabead complex andincubated with gentle agitation for 20 minutes at room temperature. Thebeads and immunoprecipitated complexes were magnetically collected andwashed three times with PBS. A sample of the unbound fraction was savedand the immunoprecipitated material was eluted by resuspension in 4×SDSPAGE sample buffer. Samples were analyzed by immunoblotting.

Subcellular Fractionation

Subcellular fractionation was performed using the QProteome CellCompartment kit (Qiagen) according to the supplied protocol. Allfractions were analyzed by immunoblotting for the CEP290 truncationsbeing tested and for the indicated fractionation controls and quantifiedby densitometric analysis using ImageJ 1.44p.

Recombinant Protein Expression and Purification

6×His tagged CEP290 truncation M and N were expressed from pDest-527 inE. coli BL21(DE3)pLysS (Invitrogen) and purified using the Ni-NTA FastStart Kit (Qiagen) according to the manufacturer's protocol. Purifiedprotein products were subjected to SDS-PAGE and stained with CoomassieBrilliant Blue to assess purity and determine protein concentration.

Liposome Flotation Assay

100 nm liposomes (total lipid concentration of 5 mg/mL in PBS) with alipid composition of a 60:40 molar ratio of phosphatidylserine tocholesterol were purchased from Encapsula NanoSciences and used within 2weeks of their formulation. 20 μL (1.5 μg) of recombinant CEP290truncation N, or an equivalent amount of BSA, was incubated with 230 μLof liposomes, or an equal volume of PBS alone, at 37° C. for 30 minutes.Each reaction was then mixed 1:1 with a solution of 80% sucrose in PBSand added to the bottom of a 2 mL ultracentrifuge tube. Reactions wereoverlaid with 1.3 mL of 30% sucrose in PBS, which was in turn overlaidwith 200 pt of PBS. Liposomes and liposome associated protein wereinduced to float to the top of the gradient by centrifugation at100,000×g for 90 minutes at 30° C. Five 400 pt fractions were taken,starting at the top of sucrose gradient, and equal amounts of each wereanalyzed by SDS-PAGE and western blotting, probing for either the 6×Histag or BSA.

In Vitro Transcription and Translation Reactions

Plasmid DNA was transcribed and translated using the TNT T7 reticulocytelysate system (Promega) according to the manufacturer's protocol.

Microtubule Polymerization

Pure bovine tubulin (Cytoskeleton) was diluted 1:1 in BRB80 buffer (80mM Pipes, 1 mM MgCl₂, 1 mM EGTA, pH 6.8) and cleared of insolublematerial by centrifugation at 20,000×g for 10 minutes. The solublefraction was supplemented with 1 mM GTP and incubated at 37° C. for 15minutes to polymerize microtubules. The polymerized microtubules werethen treated with 10 μM taxol and incubated at room temperature for afurther 15 minutes to stabilize the microtubules. Microtubules were thenpelleted at 48,000×g for 30 minutes at 30° C. and resuspended in BRB80supplemented with 1 mM GTP and 10 μM taxol. Microtubules were usedwithin one week of preparation.

Microtubule Binding Assays

Crude TNT T7 reaction products were diluted 1:1 in BRB80 supplementedwith 1 mM GTP and 10 μM taxol. The diluted products were then incubatedat 30° C. for 30 minutes in either the presence or absence of pure,pre-polymerized microtubules. Reactions were then centrifuged through a40% sucrose cushion at 48,000×g for 30 minutes, the supernatant wascollected, and the pellet washed once with warm BRB80 and resuspended in1×SDS PAGE sample buffer. Both fractions were subjected to SDS-PAGE andtransferred to nitrocellulose. The presence of tubulin in the pelletswas confirmed by Ponceau staining, and GFP-tagged CEP290 constructs weredetected by immunoblotting.

For microtubule binding assays performed on mouse brain homogenate, 0.5g of mouse brain was mechanically homogenized in 0.5 mL of 1% NP40 inBRB80 buffer containing a protease inhibitor cocktail. The homogenatewas cleared of insoluble material by centrifugation at 48,000×g for 30minutes at 4° C., and the resulting supernatant was either usedimmediately or snap-frozen at to 80° C. for later use. Homogenates wereincubated either at 37° C. for 30 minutes with 1 mM GTP and 10 μM taxolto promote microtubule polymerization, or at 4° C. for 30 minutes toinhibit microtubule polymerization. The resulting reactions were thenlayered over a 40% sucrose cushion, centrifuged at 48,000×g for 30minutes to pellet the microtubules and microtubule-associated proteins,and processed as above.

For the direct microtubule binding assay, 1 μM of recombinantlyexpressed and purified 6×His tagged CEP290 truncation M was incubated at30° C. for 30 minutes with increasing amounts of pure, prepolymerizedmicrotubules. Reactions were centrifuged and subjected to SDS-PAGE asabove, and tubulin and CEP290 truncation M were detected by Coomassieblue staining.

Bioinformatic Analysis

The helical wheel projection in FIG. 2E was adapted from the HelicalWheel Projection applet available atrzlab.ucr.edu/scripts/wheel/wheel.cgi. The multiple sequence alignmentwas adapted from GeneDoc 2.7.000.

Statistical Analysis

The statistical significance of the difference between two means wasdetermined using a two-tailed Student's t-test. The statisticalsignificance of the difference between three or more means wasdetermined using a two-way ANOVA and Tukey's HSD test. Statisticalanalysis was performed using GraphPad Prism Software 5.0b. p-values<0.05 were considered significant.

Example 2—CEP290 Associates with ARL13B Positive Cellular Vesicles Viaits N-Terminus

Mutations in the CEP290 gene have been implicated in a variety of humandiseases, but their effects on protein function have not yet beencharacterized. Mutations clustering in particular regions of the genemight be indicative of important functional domains, but no mutationalhotspots or functional domains have been identified to date (FIG. 1A).To understand the role CEP290 plays in cilium function, ciliogenesis,and human disease, a structure-function analysis was performed using apanel of truncation constructs spanning the full length of CEP290 inorder to identify and define domains of novel functionality.

The first two CEP290 truncations displayed distinct localizationpatterns. When overexpressed as GFP fusion proteins, the N-terminalfragment of CEP290 (spanning aa 1 to 580) showed an exclusivelyvesicular localization pattern while the C-terminal fragment of CEP290(from aa 580 to the end of the protein, aa 2479) (SEQ ID NO: 60) showeda striking fibrillar localization pattern (FIG. 1B). Both of thesepatterns were occasionally observed in cells overexpressing the fulllength CEP290 construct, but not with the same frequency as in cellsexpressing the truncations (data not shown).

Two additional truncations of the N-terminal region of the protein weregenerated to better define the domain responsible for the vesicularlocalization. The truncation spanning CEP290 aa 1 to 362 showed avesicular pattern of localization similar to that observed for thecomplete N-terminal fragment, while the truncation spanning aa 380 to580 (SEQ ID NO: 61) was present only diffusely throughout the cytoplasm(FIG. 1B). Further truncation of the protein was not effective inresolving its membrane association property beyond aa 1 to 362, implyingeither that this is the minimum region needed for CEP290 membraneassociation or that further truncation significantly interferes withprotein function.

The CEP290-positive vesicles observed by microscopy were found todisplay robust co-staining with ARL13B (FIG. 1B), a membrane proteinimportant in the trafficking of vesicles to the primary cilium. Tobiochemically assay this colocalization, detergent free post-nuclearsupernatants of cells expressing our CEP290 truncations were preparedand ARL13B positive vesicles were magnetically immunoprecipitated andanalyzed by western blotting. Both CEP290 aa 1 to 580 and CEP290 aa 1 to362 were significantly enriched in the ARL13B immunoprecipitate, whileneither CEP290 aa 380 to 580 nor GFP alone were found in significantquantities (FIG. 1D).

Thus, CEP290 aa 1 to 362 were found to be necessary and sufficient tomediate CEP290 localization to ARL13B positive cellular vesiclesrelevant to primary cilium biology. In only very few cases did theCEP290-positive vesicles exhibit any containing with LAMP2, a marker ofthe lysosomal compartment (FIG. 2A), indicating that CEP290 vesicularlocalization was not an artifact of protein overexpression.

To confirm that the vesicular structures observed by microscopy weretruly membranous organelles and not aggregates of overexpressed proteinwe performed a series of membrane co-flotation assays on cellsexpressing CEP290 aa 1 to 580. More than ⅓ of total CEP290 aa 1 to 580was found to co-float in the membrane-associated fractions (FIG. 1C),indicating that a substantial portion of the protein was, in fact,associated with cellular membranes. ARL13B was found to co-float in thesame fractions as CEP290 aa 1 to 580, corroborating the colocalizationbetween the two that we had observed by microscopy and co-IP (FIG. 1C).The dual distribution of CEP290 aa 1 to 580 within both themembrane-associated and soluble fractions along with the absence of asignal peptide from CEP290's amino acid sequence was suggestive ofperipheral, rather than integral, membrane association. To confirm this,membrane fractions of cells transfected with our CEP290 truncations wereprepared and peripheral membrane proteins were eluted from the membranewith a high pH buffer. The remaining integral membrane proteins weresubsequently solubilized with detergent. For both CEP290 aa 1 to 580 andaa 1 to 362 the majority of each truncation was found in the peripheralmembrane protein fraction (FIG. 1E). This same pattern was observed forthe peripheral membrane protein Annexin A2 (36), while the majority ofthe Na/K ATPase, an integral membrane protein, was found in the integralmembrane protein fraction (FIG. 1E). CEP290 aa 380 to 580, on the otherhand, was not found in significant amounts in either fraction. Takentogether, these data indicate that CEP290 aa 1 to 362 are necessary andsufficient for robust peripheral membrane association.

Example 3—CEP290's Capacity for Membrane Association is Increased byTruncation of its C-Terminus

To further investigate CEP290's membrane association, a series ofsubcellular fractionation experiments on cells expressing each of ourCEP290 truncations was performed. The CEP290 truncation spanning aa 580to 2479 that produced a fibrillar localization pattern by microscopy wasfound almost exclusively in the cytoskeletal fraction, while truncationslacking this region were completely absent from the cytoskeletalfraction (FIG. 2B). On the other hand, truncations that included CEP290aa 1 to 362 were again found to be significantly present in the membranefraction when compared to either GFP alone or our fractionation controls(FIG. 2B). For both CEP290 aa 1 to 580 and aa 1 to 362, roughly 30% ofeach truncation was found to be associated with cellular membranes (FIG.2C), demonstrating again that CEP290 aa 1 to 362 are necessary andsufficient for membrane association. Interestingly, a small amount offull length CEP290 was also found in the membrane fraction (FIG. 2B toC). This distribution agrees with what was observed by fluorescencemicroscopy—specifically, that full length CEP290 occasionally displayedvesicular localization, but to a lesser extent than CEP290 truncationslacking the C-terminus of the protein but containing aa 1 to 362.

Example 4—CEP290 Directly Binds Membranes In Vitro and Contains a HighlyConserved Membrane Binding Amphipathic α-Helix Motif

To determine whether CEP290's membrane association was mediated by adirect or indirect membrane interaction a series of liposomeco-flotation assays were performed on purified recombinant CEP290 aa 1to 580. CEP290 aa 1 to 580 associated with liposomes robustly, with amajority of the protein found in the liposome-associated fraction (FIG.2D). Flotation of the truncation occurred only in the presence ofliposomes, and liposome co-flotation was not observed for a controlprotein, BSA (FIG. 2D). The ability of this region of CEP290 to directlybind liposomes suggests that the observed association between theN-terminus of CEP290 and cellular membranes is mediated by a directinteraction.

Projecting CEP290 aa 1 to 362 onto an α-helical wheel indicated that asegment from aa 257 to 292 was predicted to form a canonical amphipathicα-helix (FIG. 2E). Such helices have been shown to be critical inmediating robust interactions between peripheral membrane proteins andvarious cellular membranes. Comparing this stretch of the protein acrossa variety of species, we found the amphipathic helix motif to be veryhighly conserved. An examination of a sequence alignment of aa257 to 292from a variety of species shows that where there was divergence in theamino acid sequence from the sources of CEP290 aa 257 to 292 for thefollowing species: Gallus SEQ ID NO: 35, Meleagris SEQ ID NO: 36, RattusSEQ ID NO: 37, Mus SEQ ID NO: 38, Pongo SEQ ID NO: 39, Macaca SEQ ID NO:40, Homo sapiens SEQ ID NO: 41, Felis SEQ ID NO: 42, Ailuropoda SEQ IDNO: 43 and Danio SEQ ID NO: 45, there was usually conservation ofpolarity and charge between the divergent residues. Taken together,these data support that the highly conserved amphipathic helix locatedwithin the membrane binding region of CEP290 mediates CEP290's novelmembrane binding function.

Example 5—CEP290 AA 1695 to 1966 Mediate Colocalization withMicrotubules

CEP290 aa 580 to 2479 appeared both by microscopy and subcellularfractionation to be associated with the cytoskeleton (FIG. 1B, 2A). Tofurther investigate this phenomenon, we constructed a library ofadditional CEP290 truncations to thoroughly interrogate CEP290'scytoskeletal association (FIG. 3B). Overexpression of these truncationsas GFP fusions revealed that those truncations containing CEP290 aa 1695to 1966, referred to as region M, displayed a fibrillar localizationpattern similar to that which was observed for CEP290 aa 580 to 2479(FIG. 3A, B). The fibrils formed by these CEP290 truncations were notedto co-localize with the microtubule network. Truncations lacking CEP290region M never display any fibrillar localization (FIG. 3A, B). Thisalong with the fact that CEP290 region M alone showed robustcolocalization with the tubulin network implicated CEP290 region M asnecessary and sufficient for microtubule co-localization.

The degree to which different CEP290 truncations displayed a fibrillarlocalization pattern was found to be dependent upon which regions of theprotein were included in the truncation. The full length CEP290construct was noted to produce a fibrillar localization pattern in onlyabout 10% of transfected cells (FIG. 3C). Truncations lacking either theN- or C-terminus of CEP290, on the other hand, were found to displayfibrillar localization in roughly 20% and 60% of transfected cells,respectively. The truncation lacking both termini was found to display afibrillar localization pattern in nearly 80% of transfected cells. Thesedata indicated that the N- and C-termini of the protein have aninhibitory or regulatory effect on CEP290's microtubule binding ability.All of our truncations displayed co-localization with pericentrin, amarker of the centriole (the normal site of CEP290 localization) (FIG.3A, insets). Homotypic interactions between endogenous CEP290, presentat the centrioles, and our truncations (through CEP290'shomo/heterodimerization domains, found within either terminus of theprotein (29)) might explain the observed centriolar localization of anumber of our truncations. However, those truncations lacking bothhomo/heterodimerization domains are apparently still capable oflocalizing to the centriole, implying that multiple regions throughoutCEP290 are capable of affecting centriolar localization.

Example 6—CEP290 Microtubule Association Results in MicrotubuleAcetylation and Bundling

In cells transfected with CEP290 constructs containing region M therewas a dramatic increase in the intensity of acetylated α-tubulinstaining, with bundles of acetylated microtubules looping throughout thecells (FIG. 4A). These increases were not seen for truncations lackingregion M. The degree to which different CEP290 truncations increased theacetylation and bundling of microtubules was dependent upon whichregions of the protein were included in the truncation. Full lengthCEP290 and CEP290 truncations lacking either the N- or C-terminusincreased microtubule acetylation and bundling in nearly 40% oftransfected cells while CEP290 truncations lacking both the N- and Ctermini of the protein increased microtubule acetylation and bundling innearly 75% of cells (FIG. 4B). Less than 15% of cells transfected withtruncations lacking region M were noted to have any change inmicrotubule acetylation or bundling.

Example 7—CEP290 Directly Binds Microtubules In Vitro

To test whether microtubule co-localization was indicative of aninteraction between CEP290 and microtubules, we performed a series of invitro microtubule co-sedimentation assays using our CEP290 truncationconstructs. Truncations containing CEP290 region M were found tosignificantly associate with microtubules in vitro, while thosetruncations lacking this region displayed no significant microtubuleassociation (FIG. 4C, D). Thus, region M was found to be necessary andsufficient to mediate robust CEP290 microtubule association. Again, thedegree to which different CEP290 truncations associated withmicrotubules was found to be dependent on the inclusion of the N- andC-termini. Less than 50% of the full length CEP290 constructs and CEP290constructs lacking either terminus were found to associate withmicrotubules, while nearly 100% of CEP290 constructs lacking bothtermini associated with microtubules (FIG. 4D). To test whether CEP290region M's microtubules association was mediated by direct microtubulebinding we recombinantly expressed and purified CEP290 region M andsubjected this protein to a series of microtubule co-sedimentationassays using increasing concentrations of microtubules (FIG. 4E, F).Region M was found to directly and robustly bind to microtubules in aconcentration dependent manner (FIG. 4F). The calculated KD of thisinteraction was found to be approximately 100 nM, an affinity comparableto those of other microtubule binding proteins (38, 39).

Example 8—the N- and C-Termini of CEP290 Cooperate to Inhibit ProteinFunction and Regulate Ciliogenesis

The observation that the N- and C-termini of CEP290 appeared to act ininhibiting the membrane and microtubule binding activity of the protein(FIG. 2B, 3C, 4B, 4D) suggested that these regions might be regulatorydomains mediating the autoinhibition of the protein. To test thishypothesis, we transduced hTERT-RPE1 cells with lentiviral vectorsencoding either the N- or C-terminal regulatory regions of the proteinand observed the cells for deficits in primary cilium formation. To oursurprise, we found that overexpression of either of these regulatoryregions resulted not in deficiencies in primary cilium formation, butinstead in significant increases in the percent of cells forming primarycilia, with more than twice as many cells forming primary cilia thanthose cells treated with a control vector (FIG. 5A, B). The length ofcilia formed by cells overexpressing either regulatory region was alsosignificantly increased by more than 25% compared to cells treated withthe control vector (FIG. 5C, D). These increases were only observed incells maintained in media supplemented with serum, a condition in whichCEP290 is normally inhibited (24), implying that these regulatorydomains act through the same pathway that mediates normal CEP290inhibition. Dysregulation of CEP290 by overexpression of eitherregulatory region was sufficient to initiate aberrant primary ciliumformation, suggesting that there is no further downstream regulation ofciliogenesis beyond CEP290. Interestingly, in both the serum starved andserum fed state it was noted that occasional cells transduced with theN-terminus of CEP290 appeared to produce multiple ciliary axonemes atthe same centrosome (FIG. 5A, 5E to 5G). These axonemes always emanatedfrom a single focus of pericentrin (FIG. 5F) and were often found at 90°to each other. In some, but not all cases, one or more of these axonemesco-stained with ARL13B (FIG. 5E), a protein associated with the ciliarymembrane (32), indicating that at least some of these multitoaxonemestructures were fully formed cilia.

Example 9—the RD16 Mouse CEP290 Gene Encodes a Version of the ProteinDeficient in Microtubule Binding

The rd16 mouse is a retinal disease model of CEP290 deficiencycharacterized by a rapid and near complete degeneration ofphotoreceptors. The rd16 mouse Cep290 gene encodes a Cep290 proteincontaining an in-frame deletion of 298 amino acids (17) that overlapsthe region of human CEP290 we identified as being critical formicrotubule binding (FIG. 6A). We generated two truncation mutants ofhuman CEP290 containing either the region of the microtubule bindingdomain deleted in the rd16 mouse, or the region of the microtubulebinding domain spared by the mouse deletion (FIG. 6A) to test whethermicrotubule binding might be impaired by the rd16 deletion. To oursurprise, when overexpressed in hTERT-RPE1 cells, both truncationsdisplayed a diffuse localization pattern indicative of a primarilycytosolic localization (FIG. 6B).

In neither case was any significant co-localization with the microtubulenetwork observed. We confirmed that neither of these constructs wascapable of associating with microtubules by subjecting them tomicrotubule co-sedimentation assays (FIG. 6C). Neither construct wasfound to significantly co-sediment with microtubules compared to theno-microtubule control (FIG. 6D), indicating both that the rd16 deletionperturbs microtubule binding and that microtubule binding is conferredby a larger portion of the CEP290 gene than was included in either ofour truncations.

To confirm that rd16 Cep290 was in fact deficient in microtubule bindingwe subjected brain lysates from wild type (WT) and rd16 mice tomicrotubule co-sedimentation assays (FIG. 6E). WT Cep290 showed verysignificant microtubule association, with roughly 60% of the proteinassociating with microtubules (comparable to full length human CEP290(FIG. 4D)), while rd16 Cep290 was found to be completely deficient inmicrotubule binding (FIG. 6F).

Example 10—the RD16 Mouse is Deficient in Cilium Formation and Structure

While the retinal phenotype of the rd16 mouse has been well documented(40), no cellular phenotype regarding primary cilium formation orstructure has yet been reported. To investigate the effect that ablationof Cep290 microtubule binding might have on primary cilium formation, weassayed primary dermal fibroblasts from rd16 and WT mice fordeficiencies in cilium formation and structure. In both serum starvedand serum fed conditions, rd16 fibroblasts were found to besignificantly deficient in primary cilium formation, with roughly 50%fewer cells forming cilia than WT controls (FIG. 7A to C). The ciliaproduced by rd16 fibroblasts were also found to be more than 25% shorterthan those produced by WT fibroblasts (FIG. 7D, E), further suggestingthat the microtubule binding functionality of CEP290 is criticallyimportant in the maintenance and formation of the primary cilium and,when disrupted, capable of causing severe retinal disease.

Discussion of Examples 1 to 10

CEP290 acts as a bridge between the ciliary membrane and the microtubuleaxoneme. To date, how CEP290 functions as a component of the ciliaryY-links has been unclear. The inventors have shown that CEP290 iscapable of directly binding to both ciliary membranes and microtubules,anchoring the two to each other and likely playing a key structural rolein the maintenance of the cilium. Furthermore, particular domains ofCEP290 responsible for mediating these specific functions have beenidentified. The N-terminus of the protein, containing a highly conservedamphipathic helix, mediates CEP290's membrane binding activity. Multipleexperiments determined that a region near the C-terminus of CEP290,encompassing much of the protein's myosin-tail homology domain, wasnecessary and sufficient to mediate microtubule binding.

The location of these two functional domains at opposite ends of CEP290immediately supports an important structural role for the protein,anchoring the ciliary membrane to the axoneme at a fixed distance, whichis likely critical to the process and regulation of IFT. In addition tobinding microtubules, CEP290 is capable of mediating their acetylationand bundling, two hallmarks of the microtubules that make up the ciliaryaxoneme, suggesting that CEP290 likely plays an important role in thestabilization, bundling, and organization of microtubules duringciliogenesis.

This data and analysis of CEP290's membrane and microtubule bindingactivities provides evidence that the full length protein exhibitedattenuated activity when compared to truncation mutants lacking the N-or C-terminus. Confirming a role for these domains in the regulation ofthe protein's function and ciliogenesis, we found that overexpression ofeither domain interfered with the normal regulation of CEP290 and wassufficient to initiate aberrant primary cilium formation. Thisdemonstrates that there is no further downstream regulation ofciliogenesis beyond CEP290. Overexpression of the regulatory regions inserum-starved cells, where CEP290 is known to be relieved of inhibition,did not result in any increase in CEP290 activity, implying that theseregulatory domains act through the same pathway that mediates normalCEP290 inhibition.

These data support a definition for a mechanism of CEP290 regulation. Inone case, both regulatory loci could be acted upon by extraneousinhibitory factors to mediate CEP290 inhibition. In fact, it has beenshown that the protein CP110 acts as just such an inhibitory factor,binding to the N-terminus of CEP290 and inhibiting protein activity (18,19). Accordingly, we found that, in some cells, overexpression ofCEP290's N-terminus led to the growth of multiple ciliary axonemes. Thisis consistent with what would be expected upon competition betweenendogenous CEP290 and the overexpressed N-terminal fragment for CP110,normally removed from only one end of one centriole to initiateciliogenesis. Nonspecific depletion of CP110 from both ends of bothcentrioles by the overexpressed N-terminus could have resulted in thegrowth of multiple ciliary axonemes in the cells we observed.

If inhibition were solely dependent on the binding of a finite pool ofendogenous inhibitory factor, then overexpression of the full lengthprotein should result in competition for the inhibitory factor and onlyminimal, if any, observed inhibition of the overexpressed protein.Additionally, we would not expect to see inhibition of the full lengthconstruct in in vitro assays where inhibitory factors should not bepresent at meaningful concentrations. In all our experiments assessingprotein activity, we found that full length CEP290 was significantlyinhibited compared to truncation mutants lacking the novel inhibitoryregions, arguing against extraneous factors such as CP110 being solelyresponsible for CEP290 regulation.

Without wishing to be bound by theory, we propose an alternative modelfor CEP290, i.e., the two novel regulatory regions of the proteincooperate to inhibit CEP290 function, binding to each other and causinga conformational change in the protein, stabilized by the binding ofCP110, that obscures important functional domains and decreases proteinfunction (FIG. 8). Thus, the overexpression of either regulatory domainwould saturate endogenous CEP290 regulatory domains, preventing theprotein from homotypically binding to itself and resulting in aparadoxical increase in protein function. Similarly the full lengthprotein, of its own accord, would be expected to display innateinhibition regardless of the experimental conditions used. These areexactly the results we observed in all of the examples.

CEP290's amphipathic helix falls within the N terminal regulatory regionwe have identified, positioning it appropriately to play a similar rolein the autoinhibition of the protein. Additionally, the microtubulebinding region we have identified is immediately adjacent to andpotentially a component of the novel C-terminal inhibitory domain. Thismechanism of autoinhibition, conserved among membrane-actin cytoskeletonbridging proteins, is likely operative and conserved for membrane tomicrotubule bridging proteins as well. CEP290 would be the first proteinin this class shown to rely upon this mechanism of inhibition.

This model is also supported by observations made in the rd16 mouse,such as the apparent increased affinity of rd16 Cep290, compared to WT,for RPGR. The rd16 deletion of the microtubule binding/regulatory regionmay thus result in decreased autoinhibition and a higher affinity ofCep290 for its interacting partners, as was observed.

Numerous organ systems are affected by CEP290 deficiencies. Themicrotubule binding function of CEP290 is clearly of critical importanceto the function of the protein on a cellular level and, critical indisease. The rd16 mouse Cep290 gene was found to encode a version of theprotein completely deficient in microtubule binding. This mouse modelalso exhibits significant deficits in primary cilium formation anddramatic and rapid retinal degeneration, implying that deficiencies inmicrotubule binding can lead to significant pathology. In fact, over 24unique mutations identified in human CEP290 patients map to the novelmicrotubule binding domain we report here (FIG. 1). Almost all of thesemutations are expected to have truncating effects on the protein, which,as in the rd16 mouse, would result in significant deficiencies inmicrotubule binding. These truncated effects can explain the mechanismunderlying the disease phenotype seen in these individuals.

Example 11: Creation of a CEP290 Knockdown Cell Line

To test the efficacy of our miniCEP290 therapeutic we first set out tocreate a CEP290-knockdown reporter cell line. Knockdown of CEP290 incultured cells has been reported to result in dramatic decreases inciliation upon serum starvation, and rescue of this phenotype serves asa good reporter for miniCEP290 protein function. Three CEP290 shRNAconstructs were generated and transfected into hTERT-RPE1 cells toassess their ability to knockdown levels of CEP290 protein. One weekpost transfection cell lysates were collected and assayed for CEP290 bywestern blotting. All three constructs were found to affect a greaterthan 50% reduction in CEP290 protein levels, even in only transienttransfection (FIGS. 12A, 12B). To assay the effects of each of theseconstructs on cell ciliation, retrovirus vectors encoding each constructwere generated and used to transduce hTERT-RPE1 cells. Control andtransduced cells were stained for acetylated tubulin and observed byfluorescence microscopy for deficits in ciliation. Construct sh2 inparticular was found to affect a profound decrease in cell ciliation,with only 50% of cells forming primary cilia, compared to 75% of controlcells, upon serum starvation (FIG. 12C, 12D).

We selected CEP290 shRNA construct 2 due to its efficiency in knockingdown CEP290 protein levels and ability to affect a significant ciliaryphenotype. CEP290 sh2 retrovirus-transduced hERT-RPE1 cells wereselected for with puromycin and individual clones were isolated andassayed for CEP290 levels. All of the clones tested were found toexhibit significant knockdown of CEP290 (FIG. 13A), but clones 2.5, 2.7,and 2.8 were each found to affect the greatest knockdown, with less than30% of endogenous CEP290 remaining (FIG. 13B). To test the ciliaryphenotype of such significant knockdown of CEP290 protein, clonal lines2.5, 2.7, and 2.8 were stained for acetylated tubulin, a marker of theprimary cilium, and assayed by fluorescence microscopy for ciliation.Clone 2.8 in particular was characterized by a remarkably severe deficitin ciliation upon serum starvation (FIG. 13C), with only 5% of sh2.8cells producing primary cilia, compared to greater than 75% of controlcells (FIG. 13D). In the serum fed state, sh2.8 cells formed cilia onlyextremely rarely, making accurate quantification difficult (data notshown). CEP290 shRNA 2.8 cell line was selected as a reporter forminiCEP290 gene rescue.

Example 12—Design of a miniCEP290 Gene

To design a miniCEP290 gene small enough to fit within AAV's limitedpackaging capacity and to maintain as much of the protein as possible,CEP290 amino acids 130-380, 700-1040, 1260-1605, and 1695-1990 wereincluded, making for a total open reading frame of only 3.7 kb, smallenough for AAV packaging (FIG. 14A, 14B). MiniCEP290 was thusstrategically designed to include CEP290's membrane and microtubulebinding domains and almost all of CEP290's PCM-1, NPHP5, CC2D2A, andRab8A binding domains, while leaving out as much of CEP290's knownautoregulatory domains as possible. The mini gene was codon optimized,both to increase expression levels and to harden the transcript againstthe effects of the shRNA used to generate the CEP290 knockdown reportercell line, and synthesized by DNA 2.0.

Example 13—miniCEP290 Localizes Correctly in HTERT-RPE1 Cells

As a preliminary test of miniCEP290's ability to recapitulate CEP290functionality, a GFP-fused miniCEP290 expression construct was created.Upon transfection into hTERT-RPE1 cells, miniCEP290 was found tolocalize to discrete puncta throughout the cytoplasm (FIG. 14C), apattern similar to that observed for overexpressed full-length CEP290.In cells where primary cilia were present, a punctus of miniCEP290 wasalways found exactly at the ciliary transition zone, immediately betweenthe ciliary axoneme and centrosome (as indicated by acetylated tubulinand pericentrin staining, respectively; FIG. 14C), indicating that, atleast in cells with endogenous CEP290 expression, miniCEP290 was capableof correctly localizing to the same compartment as its full-lengthcounterpart.

MiniCEP290 localizes appropriately in hTERT-RPE1 cells and doesn't seemto interfere with ciliogenesis, an important concern when overexpressingtruncation mutants. To determine whether miniCEP290 is also capable ofbinding to microtubules and cellular membranes, two functions recentlydiscovered to be critical to full-length CEP290's role in ciliumformation, a panel of immunoprecipitation experiments is performed toconfirm that the minigene is capable of interacting with known CEP290binding partners, an aspect of CEP290 biology important to the protein'sfunction at the cilium. The miniCEP290 gene is subcloned into alentiviral vector to assess its ability to rescue the ciliogenesisphenotype of the sh2.8 cell line.

Results in cell culture are validated in animal models to demonstratetherapeutic use. The lentiviral vectors are tested in early postnatalrd16 mice as this leads to transduction of at least some photoreceptorprecursor cells. Also, AAV vectors encoding the miniCEP290 gene aregenerated and subretinally administered to rd16 mice. Since miniCEP290recapitulates some of full-length CEP290's function, we anticipate atleast partial correction of the rd16 retinal degeneration phenotype inthe treated eyes.

Example 14: In Vivo Studies in a CPE290 Mutant Animal

For in vivo studies, virus is delivered subretinally or intravitreallyunder direct surgical visualization using methods described previously(Bennett, J., et al. 1999 Proc. Natl. Acad. Sci. USA 96, 9920-9925 andBennett, J. et al, 2000 Meth. Enzymol. 316, 777 to 789). Eyes from threeanimals, e.g., mice or dogs, are injected either subretinally orintravitreally with an AAV8bCEP290 vector or AAV2/5 CEP290 vector, eachcontaining the minigene CEP290 of SEQ ID NO: 5 under control of therhodopsin kinase promoter. Control eyes are untreated. Other animals arekept as untreated controls.

The compositions containing the AAV vectors in isotonic sodium chloridesolution are administered by subretinal injection at suitableconcentrations—for larger animals about 1.5×10¹¹ vg/ml in volumes of 150to 400 μl and in smaller concentrations or volumes for mice. Anydetachments are anticipated to resolve spontaneously within 24 hours.Animals are evaluated post-operatively for evidence of ocular orsystemic toxicity, virus exposure to extraocular tissue, virus shedding,unfavorable immune response or other untoward effects. None is expectedto be found.

Eyes are evaluated clinically at regular intervals following the surgeryto identify inflammation. Humoral and intraocular antibodies specific toAAV capsid proteins are evaluated as described in Bennett, J., et al.1999 Proc. Natl. Acad. Sci. USA 96, 9920 to 9925, incorporated herein byreference. Hematology and blood chemistries are expected to reveal noevidence of systemic toxicity.

To correlate transgene expression with changed visual function, onesubretinally injected eye is surgically enucleated 99 days postinjection. The eyecup is divided into temporal-superior,temporal-inferior, nasal-superior, and nasal-inferior quadrants. Fromeach quadrant, the retina, and photoreceptor cells are separatelyharvested and dissected under RNase free conditions and rapidly frozen.Total RNA is prepared from these cells using the TRIzol Reagent kit(Life Technologies, Gaithersburg, Md.). DNA is extracted from the sametissues according to the vendor's protocol. cDNA is amplified from totalRNA using RNA PCR kit (Perkin Elmer, Foster City, Calif.) and theconditions listed above.

Genomic PCR demonstrates persistence of transferred viral DNAphotoreceptor cells. From noninfected cells of the affected animal, onlymutant product amplifies, but several days posttransfection in vitro theCEP290 minigene should yield the overwhelming product.

RT-PCR (figures not shown) demonstrates expression of CEP290 minigenemessage in photoreceptor cells. PCR analyses of serum and tear fluidshow no sign of virus shedding after injection. Reverse transcriptase(RT)-PCR on sera, conjunctiva, eyelids, the gland of the third eyelid,and the optic nerve from the enucleated eye of BR29 are anticipated tobe negative for the transgene many days post injection, indicating thatvirus escape to extraocular tissues is below detectable levels.

Retinal and visual function testing is then conducted usingelectroretinograms (ERGS). The physiological consequences of thetreatments are assessed by electroretinography (ERG) (Banin, E., et al.1999 Neuron 23, 549 to 57). Animals are dark-adapted (overnight),premedicated with acepromazine (0.55 mg/kg, IM) and atropine (0.03mg/kg, IM) and anesthetized by intermittent ketamine (15 mg/kg, IV,repeated every 15 minutes). Pulse rate, oxygen saturation andtemperature are monitored throughout. The cornea is anesthetized withtopical proparacaine HCl (1%) and pupils dilated with cyclopenylate (1%)and phenylephrine (2.5%).

Full field ERGs are recorded using a computer-based system (EPIC-XL, LKCTechnologies, Inc., Gaithersburg, Md.) and Burian-Allen contact lenselectrodes (Hansen Ophthalmics, Iowa City, Iowa) (Banin, E., et al. 1999Neuron 23, 549-57). Dark-adapted luminance-response functions areobtained with blue (Wratten 47A) flash stimuli spanning ˜6 log units(−2.9 to +2.8 log scottocd·s·m⁻²).

ERG b-wave amplitudes are measured conventionally from baseline ora-wave trough to positive peak; a-wave amplitude is measured frombaseline to negative peak at the maximal stimulus. For isolating conepathway function, animals are light-adapted and 29 Hz flicker ERGsevoked with white flash stimuli (0.4 log cd·s·m⁻²) on a background (0.8log cd·m⁻²); amplitudes are measured between successive negative andpositive peaks and timing from stimulus to the next positive peak.Ocular axial length and pupil diameter are measured for each experimentto permit calculation of retinal illuminance.

The restoration of retinal/visual function in the experimental model bysubretinal AAV to RPE65 is demonstrated by the results of theabove-described ERGs. A comparison of dark-adapted ERGs evoked byincreasing intensities of blue light stimuli in a control animal withERGs to the same stimuli in the disease model animal shows the affectedanimal has elevated thresholds, reduced amplitudes and waveform shapechanges (i.e., b-waves but no detectable a-waves). Over a 5 log unitrange of increasing stimulus intensity, the ERG of normal animals areanticipated to respond with increasing amplitude of bipolar cell(b-wave) and photoreceptor (a-wave) components. At all intensities thesesignals are dominated by rod photoreceptor retinal pathways. Compared tonormal animals, the threshold stimulus required to elicit an ERGresponse from model animals is elevated.

Retinal function is improved in eyes treated with subretinal AAV toCEP290, compared to pretreatment recordings. After subretinal AAV toRPE65 therapy, the mutant animal is anticipated to show an improvedb-wave threshold, a large increase of a- and b-wave amplitudes (althoughnot to normal levels) and an ERG waveform shape that is similar tocontrols.

The details of photoreceptor function are analyzed by the amplitude andtiming of the ERG photoresponses evoked by 2.8 log scottocd·s·m⁻²flashes. All eyes with subretinal AAV-CEP290 fragment treatment recovercone flicker responses. Cone flicker ERGs are readily recordablepost-treatment).

Transmission of retinal activity to higher visual pathways isdemonstrated by pupillometry. Animals are dark-adapted for more than 3hours and pupil responses are obtained sequentially from each eye usingfull-field green stimuli (−3.2 to +3.0 log scot-cd·m⁻²) of ˜2 secondduration. Pupils are imaged with a video camera under infraredillumination and continuously recorded on a VCR. Dynamic changes inpupil diameters are measured from single frames displayed on the videomonitor in relation to the timing of each stimulus. Pupil responses arecalculated by subtracting the smallest pupil diameter achieved within 2seconds after the stimulus onset from the diameter measured in the dark.

All tested pupils are expected to constrict in response to highintensity stimuli. The threshold intensity to reach a criterionpupillary response is anticipated to be improved in subretinally-treatedeyes compared with untreated eyes.

Qualitative visual assessment of treated animals is performed at postinjection using an obstacle course and observers masked to theexperimental design. Visual behavior is also documented by videorecording. Results of behavioral testing are anticipated to beconsistent with the electrophysiological results.

Without further description, it is believed that one of ordinary skillin the art can, using the preceding description and illustrativeexamples, make and utilize the compositions of the present invention andpractice the claimed methods. While the invention has been described andillustrated herein by references to various specific materials,procedures and examples, it is understood that the invention is notrestricted to the particular combinations of material and proceduresselected for that purpose. The disclosures of T. G. Drivas et al, J ClinInvest. 2013; 123(10); 4525-4539 and U.S. provisional patent applicationNo. 61/847,016, as well as all patents, patent applications and otherreferences, including the Sequence Listing cited in this specificationare hereby incorporated by reference in their entirety.

TABLE 2 (Sequence Listing Free Text) The following information isprovided for sequences containing free text under numeric identifier<223>. SEQ ID NO: (containing free text) Free text under <223> 3Synthetic construct having codon optimization of human nucleic acidsequence for CEP290 4 Synthetic construct having codon optimization ofhuman protein sequence for CEP290 5 Synthetic Construct; nucleic acidsequence contain- ing codon optimized human CEP290 fragments splicedtogether in a single open reading frame; the nucleic acid sequencesencoding fragments aa130to380, aa700to1040; aa1260to1605 andaa1695to1990. 6 Synthetic Construct; amino acid sequence containingcodon optimized human CEP290 fragments spliced together in a single openreading frame: aa130to380, aa700to1040; aa1260to1605 and aa1695to1990.

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The invention claimed is:
 1. A method of treating a mammalian subjecthaving a disease associated with a defect in the CEP290 gene, a CEP290mutation, or a defect in the expression or levels of expression of theCEP290 protein, the method comprising administering to said subject aneffective concentration of a composition comprising: (i) a synthetic orrecombinant nucleic acid sequence encoding a truncated CEP290 proteincomprising discontinuous CEP290 fragments spliced together in a singleopen reading frame, said truncated CEP290 protein having biologicalactivity that mimics the biological activity of normal full-lengthCEP290, wherein the truncated CEP290 protein comprises the amino acidsequence of SEQ ID NO: 6; and (ii) a therapeutically acceptable orpharmaceutically acceptable carrier.
 2. The method of claim 1, whereinthe administering comprises delivering the composition by subretinalinjection to the retina or photoreceptor cells, delivering thecomposition by retrograde urethral injection to the kidney, deliveringthe composition by intra-ventricular or intra-cerebral injection to thebrain, or topically delivering the composition to nasal epithelium. 3.The method of claim 1, wherein the mammalian subject is a human.
 4. Amethod of treating a mammalian subject having a disease associated witha defect in the CEP290 gene, a CEP290 mutation, or a defect in theexpression or levels of expression of the CEP290 protein, the methodcomprising administering to said subject an effective concentration of acomposition comprising: (i) a synthetic or recombinant nucleic acidsequence encoding a truncated CEP290 protein comprising discontinuousCEP290 fragments spliced together in a single open reading frame, saidtruncated CEP290 protein having biological activity that mimics thebiological activity of normal full-length CEP290, wherein the nucleicacid sequence comprises the nucleic acid sequence of SEQ ID NO: 5; and(ii) a therapeutically acceptable or pharmaceutically acceptablecarrier.
 5. The method of claim 4, wherein the administering comprisesdelivering the composition by subretinal injection to the retina orphotoreceptor cells, delivering the composition by retrograde urethralinjection to the kidney, delivering the composition by intra-ventricularor intra-cerebral injection to the brain, or topically delivering thecomposition to nasal epithelium.
 6. The method of claim 4, wherein themammalian subject is a human.
 7. A method of treating a mammaliansubject having a disease associated with a defect in the CEP290 gene, aCEP290 mutation, or a defect in the expression or levels of expressionof the CEP290 protein, the method comprising administering to saidsubject an effective concentration of a composition comprising: (i) asynthetic or recombinant nucleic acid sequence encoding a truncatedCEP290 protein comprising discontinuous CEP290 fragments splicedtogether in a single open reading frame, said truncated CEP290 proteinhaving biological activity that mimics the biological activity of normalfull-length CEP290, wherein the discontinuous CEP290 fragments comprisethe amino acid sequence of SEQ ID NO: 49 and the amino acid sequence ofSEQ ID NO: 53; and (ii) a therapeutically acceptable or pharmaceuticallyacceptable carrier.
 8. The method of claim 7, wherein the administeringcomprises delivering the composition by subretinal injection to theretina or photoreceptor cells.
 9. The method of claim 7, wherein theadministering comprises delivering the composition by retrogradeurethral injection to the kidney.
 10. The method of claim 7, wherein theadministering comprises delivering the composition by intra-ventricularor intra-cerebral injection to the brain.
 11. The method of claim 7,wherein the administering comprises topically delivering the compositionto nasal epithelium.
 12. The method of claim 7, wherein thediscontinuous CEP290 fragments further comprise the amino acid sequenceof SEQ ID NO:
 51. 13. The method of claim 7, wherein the discontinuousCEP290 fragments further comprise the amino acid sequence of SEQ ID NO:52.
 14. The method of claim 7, wherein the discontinuous CEP290fragments further comprise the amino acid sequence of SEQ ID NO: 51 andthe amino acid sequence of SEQ ID NO:
 52. 15. The method of claim 7,wherein the mammalian subject is a human.
 16. The method of claim 7,wherein the mammalian subject has shown a clinical sign of ciliopathy.17. The method of claim 7, wherein the mammalian subject has LebersCongenital Amaurosis (LCA).
 18. The method of claim 16, wherein theclinical sign comprises decreased peripheral vision, decreased centralvision, decreased night vision, loss of color perception, reduction invisual acuity, decreased photoreceptor function, or a pigmentary change.19. The method of claim 16, wherein the ciliopathy is a disorder of thebone, brain, central nervous system, kidney, or olfactory epithelia.